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Find_consistent_blocks_v3.bsh
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Find_consistent_blocks_v3.bsh
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# use this one for final results!
# only keep scripts for manuscript. A full version (might not be updated see Find_consistent_blocks_v2.bsh)
# use the significantly AlleleHMM block identify by pooling the reads from the same tissue and cross , the pat and mat in PB6 WERE corrected.
# eg: ${OR}_MB6_all_R1_${s}_regions_t1E-0${T}.sorted_binomtest_SigBlocks_IGV.bed (the pat and mat in PB6 WERE corrected)
# combine the significant alleleHMM blocks from the same tissue but different cross
# map reads from each individual sample from the same tissue and cross to the combined_cross AlleleHMM blocks
# identify blocks that have the same allele bias in all samples from the same tissue and cross
# use fishers method to combine p-value from multiple samples
cd /workdir/sc2457/F1_Tissues/Find_consistent_blocks
ln -s /workdir/sc2457/F1_Tissues/3rd_batch/map2ref/map2ref_bed/ .
mkdir HMM_bed
cd HMM_bed
## use the significantly AlleleHMM block identify by pooling the reads from the same tissue and cross , the pat and mat in PB6 WERE corrected.
T=5
for OR in BN LV SK SP
do
for s in plus minus
do
ln -s /workdir/sc2457/F1_Tissues/allelicbias-PersonalGenome_P.CAST_M.B6-${OR}_MB6_all_R1/AlleleHMM/${OR}_MB6_all_R1_${s}_regions_t1E-0${T}.sorted_binomtest_SigBlocks_IGV.bed ${OR}_MB6_HMM_${s}.bed
ln -s /workdir/sc2457/F1_Tissues/allelicbias-PersonalGenome_P.CAST_M.B6-${OR}_PB6_all_R1/AlleleHMM/${OR}_PB6_all_R1_${s}_regions_t1E-0${T}.sorted_binomtest_SigBlocks_IGV.bed ${OR}_PB6_HMM_${s}.bed
done
done
T=4
for OR in GI ST
do
for s in plus minus
do
ln -s /workdir/sc2457/F1_Tissues/allelicbias-PersonalGenome_P.CAST_M.B6-${OR}_MB6_all_R1/AlleleHMM/${OR}_MB6_all_R1_${s}_regions_t1E-0${T}.sorted_binomtest_SigBlocks_IGV.bed ${OR}_MB6_HMM_${s}.bed
ln -s /workdir/sc2457/F1_Tissues/allelicbias-PersonalGenome_P.CAST_M.B6-${OR}_PB6_all_R1/AlleleHMM/${OR}_PB6_all_R1_${s}_regions_t1E-0${T}.sorted_binomtest_SigBlocks_IGV.bed ${OR}_PB6_HMM_${s}.bed
done
done
OR=HT
for s in plus minus
do
T=4
ln -s /workdir/sc2457/F1_Tissues/allelicbias-PersonalGenome_P.CAST_M.B6-${OR}_MB6_all_R1/AlleleHMM/${OR}_MB6_all_R1_${s}_regions_t1E-0${T}.sorted_binomtest_SigBlocks_IGV.bed ${OR}_MB6_HMM_${s}.bed
T=5
ln -s /workdir/sc2457/F1_Tissues/allelicbias-PersonalGenome_P.CAST_M.B6-${OR}_PB6_all_R1/AlleleHMM/${OR}_PB6_all_R1_${s}_regions_t1E-0${T}.sorted_binomtest_SigBlocks_IGV.bed ${OR}_PB6_HMM_${s}.bed
done
# remove LG samples
#T=5
#for s in plus minus
# do
#ln -s /workdir/sc2457/F1_Tissues/allelicbias-PersonalGenome_P.CAST_M.B6-LG_MB6_FG_R1/AlleleHMM/LG_MB6_FG_R1_${s}_regions_t1E-0${T}.sorted_binomtest_SigBlocks_IGV.bed LG_MB6_HMM_${s}.bed
#ln -s /workdir/sc2457/F1_Tissues/allelicbias-PersonalGenome_P.CAST_M.B6-LG_PB6_CDE_R1/AlleleHMM/LG_PB6_CDE_R1_${s}_regions_t1E-0${T}.sorted_binomtest_SigBlocks_IGV.bed LG_PB6_HMM_${s}.bed
#done
# add KD samples
OR=KD
for s in plus minus
do
T=4
ln -s /workdir/sc2457/F1_Tissues/F1_Kidney/allelicbias-PersonalGenome_P.CAST_M.B6-${OR}_MB6_all_R1/AlleleHMM/${OR}_MB6_all_R1_${s}_regions_t1E-0${T}.sorted_binomtest_SigBlocks_IGV.bed ${OR}_MB6_HMM_${s}.bed
ln -s /workdir/sc2457/F1_Tissues/F1_Kidney/allelicbias-PersonalGenome_P.CAST_M.B6-${OR}_PB6_all_R1/AlleleHMM/${OR}_PB6_all_R1_${s}_regions_t1E-0${T}.sorted_binomtest_SigBlocks_IGV.bed ${OR}_PB6_HMM_${s}.bed
done
# how many alleleHMM blocks?
for t in BN HT SK SP KD LV GI ST
do wc -l ${t}*.bed |paste - - - - -
done
973 BN_MB6_HMM_minus.bed 1060 BN_MB6_HMM_plus.bed 715 BN_PB6_HMM_minus.bed 777 BN_PB6_HMM_plus.bed 3525 total
171 HT_MB6_HMM_minus.bed 154 HT_MB6_HMM_plus.bed 598 HT_PB6_HMM_minus.bed 638 HT_PB6_HMM_plus.bed 1561 total
385 SK_MB6_HMM_minus.bed 384 SK_MB6_HMM_plus.bed 1371 SK_PB6_HMM_minus.bed 1571 SK_PB6_HMM_plus.bed 3711 total
608 SP_MB6_HMM_minus.bed 661 SP_MB6_HMM_plus.bed 1168 SP_PB6_HMM_minus.bed 1222 SP_PB6_HMM_plus.bed 3659 total
859 KD_MB6_HMM_minus.bed 915 KD_MB6_HMM_plus.bed 583 KD_PB6_HMM_minus.bed 667 KD_PB6_HMM_plus.bed 3024 total
1140 LV_MB6_HMM_minus.bed 1134 LV_MB6_HMM_plus.bed 1761 LV_PB6_HMM_minus.bed 1902 LV_PB6_HMM_plus.bed 5937 total
528 GI_MB6_HMM_minus.bed 576 GI_MB6_HMM_plus.bed 875 GI_PB6_HMM_minus.bed 948 GI_PB6_HMM_plus.bed 2927 total
408 ST_MB6_HMM_minus.bed 412 ST_MB6_HMM_plus.bed 1272 ST_PB6_HMM_minus.bed 1363 ST_PB6_HMM_plus.bed 3455 total
# Combine AlleleHMM significantly biased blocks from MB6 and PB6(eg: comnined BN_MB6 and BN_PB6)
# remove duplicate blocks
mkdir combined_cross
for bed in *_MB6_HMM_minus.bed #*/
do t=`echo $bed |cut -d _ -f 1`
cat ${t}_PB6_HMM_minus.bed ${t}_MB6_HMM_minus.bed |grep -v "#" |awk 'BEGIN{OFS="\t"} {print $1,$2,$3, ".",".","-"}'|LC_ALL=C sort -k1,1V -k2,2n |uniq > combined_cross/${t}_HMM_minus.bed
cat ${t}_PB6_HMM_plus.bed ${t}_MB6_HMM_plus.bed |grep -v "#" |awk 'BEGIN{OFS="\t"} {print $1,$2,$3,".",".","+"}'|LC_ALL=C sort -k1,1V -k2,2n |uniq > combined_cross/${t}_HMM_plus.bed
done
for t in BN HT SK SP KD LV GI ST
do wc -l ${t}*.bed |paste - - - - -
done
1681 BN_HMM_minus.bed 1827 BN_HMM_plus.bed 3508 total
768 HT_HMM_minus.bed 791 HT_HMM_plus.bed 1559 total
1751 SK_HMM_minus.bed 1954 SK_HMM_plus.bed 3705 total
1763 SP_HMM_minus.bed 1875 SP_HMM_plus.bed 3638 total
1436 KD_HMM_minus.bed 1579 KD_HMM_plus.bed 3015 total
2883 LV_HMM_minus.bed 3003 LV_HMM_plus.bed 5886 total
1398 GI_HMM_minus.bed 1520 GI_HMM_plus.bed 2918 total
1660 ST_HMM_minus.bed 1753 ST_HMM_plus.bed 3413 total
cd ..
wait_a_second() {
joblist=($(jobs -p))
while (( ${#joblist[*]} >= 10 ))
do
sleep 1
joblist=($(jobs -p))
done
}
PL=/workdir/sc2457/alleleDB/alleledb_pipeline_mouse
MAPS=/workdir/sc2457/mouse_AlleleSpecific/mouse_genome.sanger.ac.uk/REL-1505-SNPs_Indels/PersonalGenome_P.CAST_M.B6_indelsNsnps_CAST.bam/%s_P.CAST.EiJ_M.C57BL.6J.map
FDR_SIMS=10
FDR_CUTOFF=0.1
BinomialTest(){
# BinomialTest $f $j $MAT_READ_BED $PAT_READ_BED
f=$1
j=$2
MAT_READ_BED=$3
PAT_READ_BED=$4
bedtools coverage -s -a $f -b ${MAT_READ_BED} -sorted| awk 'BEGIN {OFS="\t"; t="_"} {print $1t$2t$3, $1,$2,$3,$7,$8,$9,$10}' |LC_ALL=C sort -k1,1V -k2,2n > ${j}.mat_cov.bed &
bedtools coverage -s -a $f -b ${PAT_READ_BED} -sorted| awk 'BEGIN {OFS="\t"; t="_"} {print $1t$2t$3, $1,$2,$3,$7,$8,$9,$10}' |LC_ALL=C sort -k1,1V -k2,2n > ${j}.pat_cov.bed &
#bedtools coverage -s -a $f -b ${IDENTICAL_READ_BED} -sorted| awk 'BEGIN {OFS="\t"; t="_"} {print $1t$2t$3, $1,$2,$3,$7,$8,$9,$10}' |LC_ALL=C sort -k1,1V -k2,2n > ${j}.iden_cov.bed &
wait
# filter the block and only keep block with at lease 1 allele-specific read
join -t $'\t' -j 1 -o 1.1,1.2,1.3,1.4,1.5,2.5 ${j}.mat_cov.bed ${j}.pat_cov.bed | awk 'BEGIN{OFS="\t"} ($5+$6 >0) {print $0}' | \
awk 'BEGIN{OFS="\t"; t=","} ($5>$6) {print $2, $3, $4, "M"t$5t$6, $5, $6, "-" } ($5<$6) {print $2, $3, $4, "P"t$5t$6, $5, $6, "-"} ($5==$6) {print $2, $3, $4, "S"t$5t$6, $5, $6, "-"} ' \
| LC_ALL=C sort -k1,1V -k2,2n --parallel=30 > ${j}.merged_cov.bed
mv ${j}.mat_cov.bed ${j}.pat_cov.bed toremove
# output of BinomialTestFor_merged_cov.bed.py:(hmm+BinomialTest) if p-value <= 0.05, remain what it got from hmm (can ne M,P, or S), otherwise S.
python ${PL}/BinomialTestFor_merged_cov.bed.py ${j}.merged_cov.bed ${j}_binomtest.bed
mv ${j}.merged_cov.bed toremove
python ${PL}/FalsePosFor_merged_cov.bed.py ${j}_binomtest.bed ${FDR_SIMS} ${FDR_CUTOFF} > ${j}_binomtest_FDR${FDR_CUTOFF}.txt
awk 'NR==1 { print $0 } NR>1 && ($9+0) <= thresh { print $0 }' thresh=$(awk 'END {print $6}' ${j}_binomtest_FDR${FDR_CUTOFF}.txt) < ${j}_binomtest.bed > ${j}_interestingHets.bed
}
## map reads from each individual sample from the same tissue and cross to the AlleleHMM blocks comnined_corss from each tissue
for Head in BN HT SK SP KD LV GI ST
do
echo $Head
bed_dir=map2ref_bed
for f in ${bed_dir}/${Head}_MB6_*_R1.mat.bowtie.gz_AMBremoved_sorted_identical.map2ref.sorted.bed.gz #each samples from MB6 of the same tissue
do PREFIX=`echo $f|cut -d . -f 1`
echo $PREFIX
MAT_READ_BED=${PREFIX}.mat.bowtie.gz_AMBremoved_sorted_specific.map2ref.sorted.bed.gz
PAT_READ_BED=${PREFIX}.pat.bowtie.gz_AMBremoved_sorted_specific.map2ref.sorted.bed.gz
#IDENTICAL_READ_BED=${PREFIX}.mat.bowtie.gz_AMBremoved_sorted_identical.map2ref.sorted.bed.gz
P=`echo $PREFIX| cut -d / -f 2`
ln -s HMM_bed/combined_cross/${Head}_HMM_plus.bed ${P}_HMM_plus.bed
ln -s HMM_bed/combined_cross/${Head}_HMM_minus.bed ${P}_HMM_minus.bed
BinomialTest ${P}_HMM_plus.bed ${P}_HMM_plus ${MAT_READ_BED} ${PAT_READ_BED} &
BinomialTest ${P}_HMM_minus.bed ${P}_HMM_minus ${MAT_READ_BED} ${PAT_READ_BED} &
wait_a_second
done
for f in ${bed_dir}/${Head}_PB6_*_R1.mat.bowtie.gz_AMBremoved_sorted_identical.map2ref.sorted.bed.gz #each samples from PB6 of the same tissue
do PREFIX=`echo $f|cut -d . -f 1`
echo $PREFIX
# switch -m and -p for PB6
PAT_READ_BED=${PREFIX}.mat.bowtie.gz_AMBremoved_sorted_specific.map2ref.sorted.bed.gz
MAT_READ_BED=${PREFIX}.pat.bowtie.gz_AMBremoved_sorted_specific.map2ref.sorted.bed.gz
#IDENTICAL_READ_BED=${PREFIX}.mat.bowtie.gz_AMBremoved_sorted_identical.map2ref.sorted.bed.gz
P=`echo $PREFIX| cut -d / -f 2`
ln -s HMM_bed/combined_cross/${Head}_HMM_plus.bed ${P}_HMM_plus.bed
ln -s HMM_bed/combined_cross/${Head}_HMM_minus.bed ${P}_HMM_minus.bed
BinomialTest ${P}_HMM_plus.bed ${P}_HMM_plus ${MAT_READ_BED} ${PAT_READ_BED} &
BinomialTest ${P}_HMM_minus.bed ${P}_HMM_minus ${MAT_READ_BED} ${PAT_READ_BED} &
wait_a_second
done
done
# identify blocks share the same allele-bias in MB6 group (A,F,G) or PB6 group (B,C,D,E)
## use fishers method to combine p-value from multiple samples
## combine p-value in one file
for t in BN HT SK SP KD LV GI ST
do
R --vanilla --slave --args $(pwd) $t 0.05 < Find_consistent_blocks_v2.R &
done
wc -l *_ABconsistent* |paste - -
1373 BN_MB6_combined_R1_HMM_minus_ABconsistent.bed 1195 BN_MB6_combined_R1_HMM_minus_ABconsistent_FisherMethodP0.05.bed
1503 BN_MB6_combined_R1_HMM_plus_ABconsistent.bed 1289 BN_MB6_combined_R1_HMM_plus_ABconsistent_FisherMethodP0.05.bed
1009 BN_PB6_combined_R1_HMM_minus_ABconsistent.bed 831 BN_PB6_combined_R1_HMM_minus_ABconsistent_FisherMethodP0.05.bed
1086 BN_PB6_combined_R1_HMM_plus_ABconsistent.bed 889 BN_PB6_combined_R1_HMM_plus_ABconsistent_FisherMethodP0.05.bed
907 GI_MB6_combined_R1_HMM_minus_ABconsistent.bed 693 GI_MB6_combined_R1_HMM_minus_ABconsistent_FisherMethodP0.05.bed
964 GI_MB6_combined_R1_HMM_plus_ABconsistent.bed 743 GI_MB6_combined_R1_HMM_plus_ABconsistent_FisherMethodP0.05.bed
848 GI_PB6_combined_R1_HMM_minus_ABconsistent.bed 766 GI_PB6_combined_R1_HMM_minus_ABconsistent_FisherMethodP0.05.bed
937 GI_PB6_combined_R1_HMM_plus_ABconsistent.bed 805 GI_PB6_combined_R1_HMM_plus_ABconsistent_FisherMethodP0.05.bed
258 HT_MB6_combined_R1_HMM_minus_ABconsistent.bed 150 HT_MB6_combined_R1_HMM_minus_ABconsistent_FisherMethodP0.05.bed
251 HT_MB6_combined_R1_HMM_plus_ABconsistent.bed 149 HT_MB6_combined_R1_HMM_plus_ABconsistent_FisherMethodP0.05.bed
310 HT_PB6_combined_R1_HMM_minus_ABconsistent.bed 279 HT_PB6_combined_R1_HMM_minus_ABconsistent_FisherMethodP0.05.bed
299 HT_PB6_combined_R1_HMM_plus_ABconsistent.bed 272 HT_PB6_combined_R1_HMM_plus_ABconsistent_FisherMethodP0.05.bed
1239 KD_MB6_combined_R1_HMM_minus_ABconsistent.bed 1079 KD_MB6_combined_R1_HMM_minus_ABconsistent_FisherMethodP0.05.bed
1354 KD_MB6_combined_R1_HMM_plus_ABconsistent.bed 1193 KD_MB6_combined_R1_HMM_plus_ABconsistent_FisherMethodP0.05.bed
855 KD_PB6_combined_R1_HMM_minus_ABconsistent.bed 693 KD_PB6_combined_R1_HMM_minus_ABconsistent_FisherMethodP0.05.bed
968 KD_PB6_combined_R1_HMM_plus_ABconsistent.bed 783 KD_PB6_combined_R1_HMM_plus_ABconsistent_FisherMethodP0.05.bed
2475 LV_MB6_combined_R1_HMM_minus_ABconsistent.bed 2165 LV_MB6_combined_R1_HMM_minus_ABconsistent_FisherMethodP0.05.bed
2563 LV_MB6_combined_R1_HMM_plus_ABconsistent.bed 2222 LV_MB6_combined_R1_HMM_plus_ABconsistent_FisherMethodP0.05.bed
2558 LV_PB6_combined_R1_HMM_minus_ABconsistent.bed 2434 LV_PB6_combined_R1_HMM_minus_ABconsistent_FisherMethodP0.05.bed
2683 LV_PB6_combined_R1_HMM_plus_ABconsistent.bed 2567 LV_PB6_combined_R1_HMM_plus_ABconsistent_FisherMethodP0.05.bed
681 SK_MB6_combined_R1_HMM_minus_ABconsistent.bed 444 SK_MB6_combined_R1_HMM_minus_ABconsistent_FisherMethodP0.05.bed
700 SK_MB6_combined_R1_HMM_plus_ABconsistent.bed 444 SK_MB6_combined_R1_HMM_plus_ABconsistent_FisherMethodP0.05.bed
893 SK_PB6_combined_R1_HMM_minus_ABconsistent.bed 733 SK_PB6_combined_R1_HMM_minus_ABconsistent_FisherMethodP0.05.bed
958 SK_PB6_combined_R1_HMM_plus_ABconsistent.bed 814 SK_PB6_combined_R1_HMM_plus_ABconsistent_FisherMethodP0.05.bed
1404 SP_MB6_combined_R1_HMM_minus_ABconsistent.bed 1157 SP_MB6_combined_R1_HMM_minus_ABconsistent_FisherMethodP0.05.bed
1455 SP_MB6_combined_R1_HMM_plus_ABconsistent.bed 1181 SP_MB6_combined_R1_HMM_plus_ABconsistent_FisherMethodP0.05.bed
1431 SP_PB6_combined_R1_HMM_minus_ABconsistent.bed 1336 SP_PB6_combined_R1_HMM_minus_ABconsistent_FisherMethodP0.05.bed
1506 SP_PB6_combined_R1_HMM_plus_ABconsistent.bed 1398 SP_PB6_combined_R1_HMM_plus_ABconsistent_FisherMethodP0.05.bed
505 ST_MB6_combined_R1_HMM_minus_ABconsistent.bed 381 ST_MB6_combined_R1_HMM_minus_ABconsistent_FisherMethodP0.05.bed
505 ST_MB6_combined_R1_HMM_plus_ABconsistent.bed 380 ST_MB6_combined_R1_HMM_plus_ABconsistent_FisherMethodP0.05.bed
1158 ST_PB6_combined_R1_HMM_minus_ABconsistent.bed 1070 ST_PB6_combined_R1_HMM_minus_ABconsistent_FisherMethodP0.05.bed
1232 ST_PB6_combined_R1_HMM_plus_ABconsistent.bed 1131 ST_PB6_combined_R1_HMM_plus_ABconsistent_FisherMethodP0.05.bed
68534 total
for t in BN HT SK SP KD LV GI ST
do cat ${t}_*B6_combined_R1_HMM_plus_ABconsistent_FisherMethodP0.05.bed | awk '{OFS="\t"} NR>1 {print $1, $2, $3, "+"}' > ${t}_temp.txt
cat ${t}_*B6_combined_R1_HMM_minus_ABconsistent_FisherMethodP0.05.bed | awk '{OFS="\t"} NR>1 {print $1, $2, $3, "-"}' >> ${t}_temp.txt
echo "$t"
sort ${t}_temp.txt | uniq |wc -l
done
# No dupicates, but the blocks might overlapped
BN
2956
HT
713
SK
1972
SP
3229
KD
2580
LV
5574
GI
2151
ST
2457
# use sed to insert the first line
sed -i '1i #chrm\tchrmStart\tchrmEnd\twinP_count_all_samples\tp_value_all_samples\twinP\tp_value_Fisher\tp_value_individual_samples' *_ABconsistent*
# use a new folder (Combined_MB6andPB6) to examine the consistent blocks
cd /workdir/sc2457/F1_Tissues/ImprintingOrGenetics/Combined_MB6andPB6
ln -s /workdir/sc2457/F1_Tissues/Find_consistent_blocks/*_ABconsistent* . #*/
join_AB(){
file1=$1
file2=$2
file3=$3
cat ${file1} ${file2} |grep -v "#" | awk 'BEGIN{t="-"} {print $1t$2t$3}' |sort -k1,1|uniq > ${file1}.tmp1
join -a 1 -t $'\t' -e S -j 1 -o 1.1,2.5 ${file1}.tmp1 <(<${file1} awk 'BEGIN{OFS="\t"; t="-"} {print $1t$2t$3,$0}' | sort -k1,1) > ${file1}.tmp2
join -a 1 -t $'\t' -e S -j 1 -o 1.1,1.2,2.5 ${file1}.tmp2 <(<${file2} awk 'BEGIN{OFS="\t"; t="-"} {print $1t$2t$3,$0}' | sort -k1,1) | awk 'BEGIN{OFS="\t"} {split($1,a,"-"); print a[1],a[2],a[3], $2, $3}' > ${file3}
rm ${file1}.tmp*
}
# make a table with AB at MB6 and PB6
# assign blocks that are consistent biased in both cross to strain effect or imprinted effect
# blocks that are allelic biased in one cross, but S in the other cross, are named NA. and eliminated for later analysis
p=0.05
for f in *_MB6_combined_R1_HMM_plus_ABconsistent_FisherMethodP${p}.bed
do t=`echo $f|cut -d _ -f 1`
for s in plus minus
do
join_in1=${t}_MB6_combined_R1_HMM_${s}_ABconsistent_FisherMethodP${p}.bed
join_in2=${t}_PB6_combined_R1_HMM_${s}_ABconsistent_FisherMethodP${p}.bed
join_out=${t}_combined_HMM_${s}_ABconsistent_FMp${p}.bed
h=${t}_${s}_p${p}_effect
join_AB ${join_in1} ${join_in2} ${join_out}
grep S ${join_out} > ${h}_NA.bed
im=${h}_imprinting.bed
st=${h}_strain.bed
rm ${im} ${st}
grep -v S ${join_out} | awk -v im=${im} -v st=${st} 'BEGIN{OFS="\t"} substr($4,1,1)==substr($5,1,1) {print $0 >> im} substr($4,1,1)!=substr($5,1,1) {print $0 >> st}'
sed -i '1i #chrm\tchrmStart\tchrmEnd\tMB6_winP_count_all_samples\tPB6_winP_count_all_samples' ${join_out}
done
done
p=0.05
for head in BN SP HT SK KD ST GI LV
do for s in plus minus
do
wc -l ${head}_${s}_p${p}_effect_* |paste - - - -
done
done
884 BN_plus_p0.05_effect_NA.bed 28 BN_plus_p0.05_effect_imprinting.bed 619 BN_plus_p0.05_effect_strain.bed 1531 total
820 BN_minus_p0.05_effect_NA.bed 27 BN_minus_p0.05_effect_imprinting.bed 576 BN_minus_p0.05_effect_strain.bed 1423 total
741 SP_plus_p0.05_effect_NA.bed 7 SP_plus_p0.05_effect_imprinting.bed 912 SP_plus_p0.05_effect_strain.bed 1660 total
641 SP_minus_p0.05_effect_NA.bed 10 SP_minus_p0.05_effect_imprinting.bed 916 SP_minus_p0.05_effect_strain.bed 1567 total
291 HT_plus_p0.05_effect_NA.bed 4 HT_plus_p0.05_effect_imprinting.bed 61 HT_plus_p0.05_effect_strain.bed 356 total
281 HT_minus_p0.05_effect_NA.bed 6 HT_minus_p0.05_effect_imprinting.bed 68 HT_minus_p0.05_effect_strain.bed 355 total
772 SK_plus_p0.05_effect_NA.bed 8 SK_plus_p0.05_effect_imprinting.bed 235 SK_plus_p0.05_effect_strain.bed 1015 total
733 SK_minus_p0.05_effect_NA.bed 14 SK_minus_p0.05_effect_imprinting.bed 208 SK_minus_p0.05_effect_strain.bed 955 total
726 KD_plus_p0.05_effect_NA.bed 8 KD_plus_p0.05_effect_imprinting.bed 617 KD_plus_p0.05_effect_strain.bed 1351 total
682 KD_minus_p0.05_effect_NA.bed 12 KD_minus_p0.05_effect_imprinting.bed 533 KD_minus_p0.05_effect_strain.bed 1227 total
1011 ST_plus_p0.05_effect_NA.bed 9 ST_plus_p0.05_effect_imprinting.bed 241 ST_plus_p0.05_effect_strain.bed 1261 total
937 ST_minus_p0.05_effect_NA.bed 11 ST_minus_p0.05_effect_imprinting.bed 246 ST_minus_p0.05_effect_strain.bed 1194 total
668 GI_plus_p0.05_effect_NA.bed 5 GI_plus_p0.05_effect_imprinting.bed 435 GI_plus_p0.05_effect_strain.bed 1108 total
623 GI_minus_p0.05_effect_NA.bed 13 GI_minus_p0.05_effect_imprinting.bed 405 GI_minus_p0.05_effect_strain.bed 1041 total
915 LV_plus_p0.05_effect_NA.bed 11 LV_plus_p0.05_effect_imprinting.bed 1926 LV_plus_p0.05_effect_strain.bed 2852 total
841 LV_minus_p0.05_effect_NA.bed 15 LV_minus_p0.05_effect_imprinting.bed 1864 LV_minus_p0.05_effect_strain.bed 2720 total
# check overlap blocks of imprinting and see if there is inconsistency. eg: one MM, the other PP
#f=BN_plus_p0.05_effect_imprinting.bed
rm tmp.txt
for body in _plus_p0.05_effect_imprinting.bed _minus_p0.05_effect_imprinting.bed
do
for head in BN SP HT SK KD ST GI LV
do f=${head}${body}
wc -l $f >>tmp.txt
bedtools intersect -f 0.3 -a $f -b $f -wo | awk 'BEGIN{OFS="\t"} ($3-$2 != $NF) {print $0}' | awk 'BEGIN{OFS="\t";m=":";d="-"} (substr($4,1,1) != substr($9,1,1)) {print $1m$2d$3,substr($4,1,1),substr($9,1,1),$0}' > ${f}_overlap_incosistent
wc -l ${f}_overlap_incosistent >>tmp.txt
done
done
cat tmp.txt |paste - - # all consistent
28 BN_plus_p0.05_effect_imprinting.bed 0 BN_plus_p0.05_effect_imprinting.bed_overlap_incosistent
7 SP_plus_p0.05_effect_imprinting.bed 0 SP_plus_p0.05_effect_imprinting.bed_overlap_incosistent
4 HT_plus_p0.05_effect_imprinting.bed 0 HT_plus_p0.05_effect_imprinting.bed_overlap_incosistent
8 SK_plus_p0.05_effect_imprinting.bed 0 SK_plus_p0.05_effect_imprinting.bed_overlap_incosistent
8 KD_plus_p0.05_effect_imprinting.bed 0 KD_plus_p0.05_effect_imprinting.bed_overlap_incosistent
9 ST_plus_p0.05_effect_imprinting.bed 0 ST_plus_p0.05_effect_imprinting.bed_overlap_incosistent
5 GI_plus_p0.05_effect_imprinting.bed 0 GI_plus_p0.05_effect_imprinting.bed_overlap_incosistent
11 LV_plus_p0.05_effect_imprinting.bed 0 LV_plus_p0.05_effect_imprinting.bed_overlap_incosistent
27 BN_minus_p0.05_effect_imprinting.bed 0 BN_minus_p0.05_effect_imprinting.bed_overlap_incosistent
10 SP_minus_p0.05_effect_imprinting.bed 0 SP_minus_p0.05_effect_imprinting.bed_overlap_incosistent
6 HT_minus_p0.05_effect_imprinting.bed 0 HT_minus_p0.05_effect_imprinting.bed_overlap_incosistent
14 SK_minus_p0.05_effect_imprinting.bed 0 SK_minus_p0.05_effect_imprinting.bed_overlap_incosistent
12 KD_minus_p0.05_effect_imprinting.bed 0 KD_minus_p0.05_effect_imprinting.bed_overlap_incosistent
11 ST_minus_p0.05_effect_imprinting.bed 0 ST_minus_p0.05_effect_imprinting.bed_overlap_incosistent
13 GI_minus_p0.05_effect_imprinting.bed 0 GI_minus_p0.05_effect_imprinting.bed_overlap_incosistent
15 LV_minus_p0.05_effect_imprinting.bed 0 LV_minus_p0.05_effect_imprinting.bed_overlap_incosistent
### identify strain-effect domain and imprinting domains
#combine overlapped blocks from both plus and minus strand into domains
# pool blocks together
for body in _plus_p0.05_effect_imprinting.bed _minus_p0.05_effect_imprinting.bed _plus_p0.05_effect_strain.bed _minus_p0.05_effect_strain.bed
do
rm tmp${body}
for head in BN SP HT SK KD ST GI LV
do f=${head}${body}
cat $f |awk -v h=$head 'BEGIN {OFS="\t"}{print $1,$2,$3, h}'>> tmp${body}
done
sort-bed tmp${body} > T8${body}_sort
done
for coreBody in _p0.05_effect_strain _p0.05_effect_imprinting
do
rm T8_2Strand${coreBody}.bed
for body in _plus${coreBody}.bed _minus${coreBody}.bed
do
cat T8${body}_sort >> T8_2Strand${coreBody}.bed
done
# merge overlapped
bedtools merge -i <(sort-bed T8_2Strand${coreBody}.bed) -c 4 -o distinct -d 0 |awk 'BEGIN {OFS="\t";m=":";d="-"}{print ($3-$2)/1000000, $1m$2d$3, $0}' > T8_2Strand${coreBody}.bed_cluster
done
28 T8_2Strand_p0.05_effect_imprinting.bed_cluster
3466 T8_2Strand_p0.05_effect_strain.bed_cluster
# how many im domains ovelapped with st domains?
bedtools intersect -u -a T8_2Strand_p0.05_effect_imprinting.bed_cluster_IGV.bed -b T8_2Strand_p0.05_effect_strain.bed_cluster_IGV.bed |wc -l
15
chr10 13011734 13167371 BN,ST
chr11 11832817 12322538 BN,GI,HT,KD,LV,SK,SP,ST
chr11 22858106 23001124 BN,GI,KD,LV,SK,SP,ST
chr12 108836167 110507453 BN,GI,HT,LV,SK,ST
chr15 96991272 97163544 SK
chr17 12331162 12925535 BN,GI,HT,KD,LV,SK,SP,ST
chr18 12721540 13014732 BN,LV,SP
chr2 152654404 152741111 BN,KD,LV
chr2 168921226 169026286 LV
chr2 174080042 174325458 BN,SP
chr4 118360945 118382784 LV
chr7 112281632 112286493 SK
chr7 143041189 143511031 BN,GI,HT,KD,LV,SK,SP,ST
chr9 89791204 90054507 BN
chr9 96431959 96530231 SK
## consistent biased blocks distribution across tissue
# run scripts in UpSetR.R
# strain effect domain regardless of strandness
# imprinting domain regardless of strandness
## characterize the domains
# the size of the domain
for f in T8_2Strand_p0.05_effect_*.bed_cluster
do
cat $f | awk 'BEGIN {OFS="\t"} {print $5-$4}' > ${f}_length
done
# Histo_of_TSS_countsPerCluster.R
# how many genecode annotation?
# Histo_of_TSS_countsPerCluster.R
mkdir /workdir/sc2457/F1_Tissues/ImprintingOrGenetics/Combined_MB6andPB6/GeneAnnotationInCluster
cd GeneAnnotationInCluster
ln -s ../T8_2Strand_p0.05_effect_*.bed_cluster .
ln -s /workdir/sc2457/F1_Tissues/GeneAlleleSpecificity_old/gencode.vM20.annotation_geneMerged.bed .
# mouse mm10_GRCm38
# make bed from gtf from GENCODE
# gtf2bed < gencode.vM20.annotation.gtf > gencode.vM20.annotation.bed
# avoid multiple count of genes share similarl location, need to merge bed of overlaping genes as follows:
# cat gencode.vM20.annotation.bed | cut -f 1-8 |awk 'BEGIN {OFS="\t"} ($8=="gene"){print $0}' |LC_ALL=C sort --temporary-directory=/workdir/sc2457/tmp/ --parallel=10 -V > gencode.vM20.annotation_gene.bed
# -s option will only merge intervals that are overlapping/bookended and are on the same strand
# bedtools merge -i <(cat gencode.vM20.annotation.bed | cut -f 1-8 |awk 'BEGIN {OFS="\t"} ($8=="gene"){print $0}' |LC_ALL=C sort --temporary-directory=/workdir/sc2457/tmp/ --parallel=10 -V ) -s -o collapse,distinct,distinct -c 4,5,6 |awk 'BEGIN {OFS="\t"; a="111"} {print $1,$2,$3,$4,a,$6}'|LC_ALL=C sort --temporary-directory=/workdir/sc2457/tmp/ --parallel=10 -V > gencode.vM20.annotation_geneMerged.bed
# update to gencode.vM25.annotation.gtf
ln -s /workdir/sc2457/F1_Tissues/RNA-seq/STAR_BN/gencode.vM25.annotation.gene.bed
bedtools merge -i gencode.vM25.annotation.gene.bed -s -o distinct,distinct,distinct -c 4,5,6 |awk 'BEGIN {OFS="\t"; a="111"} {print $1,$2,$3,$4,a,$6}'|LC_ALL=C sort --temporary-directory=/workdir/sc2457/tmp/ --parallel=10 -V > gencode.vM25.annotation_geneMerged.bed
f=gencode.vM25.annotation_geneMerged.bed
bedtools intersect -wo -a <(cat ${f} |cut -f 1-3) -b <(cat T8_2Strand_p0.05_effect_imprinting.bed_cluster |cut -f 3-) |cut -f 4-7 |sort| uniq -c > ${f}_count_in_T8_2Strand_p0.05_effect_imprinting.bed_cluster
bedtools intersect -wo -a <(cat ${f} |cut -f 1-3) -b <(cat T8_2Strand_p0.05_effect_strain.bed_cluster |cut -f 3-) |cut -f 4-7 |sort |uniq -c > ${f}_count_in_T8_2Strand_p0.05_effect_strain.bed_cluster
### The switches within domains
## a strict criterium here:
# Use ONLY strain effect block in strain effect domain
# AND ONLY imprinted blocks in imprinted domain
cd /local/workdir/sc2457/F1_Tissues/ImprintingOrGenetics/Combined_MB6andPB6
mkdir StrainImprintedBlocksInDomains
cd StrainImprintedBlocksInDomains
for effect in imprinting strain
do
for head in BN SP HT SK KD ST GI LV
do
bedtools intersect -wo -a <(cat ../${head}_plus_p0.05_effect_${effect}.bed ../${head}_minus_p0.05_effect_${effect}.bed |awk 'BEGIN{OFS="\t"} {print $1, $2, $3, substr($4,1,1)}') -b <(cat ../T8_2Strand_p0.05_effect_${effect}.bed_cluster |cut -f 3-)\
|awk 'BEGIN{OFS="\t"} {print $5, $6, $7, $4}' |sort | uniq |cut -f 1-3 |uniq -c \
| awk 'BEGIN{OFS="\t"} ($1>1){print $2, $3, $4}' \
> ${head}_p0.05_effect_${effect}_IN_T8_2Strand_p0.05_effect_${effect}.bed_cluster_withABSwitches
wc -l ${head}_p0.05_effect_${effect}_IN_T8_2Strand_p0.05_effect_${effect}.bed_cluster_withABSwitches
done
done
# number of domains show switches ($1>1) in that organ
5 BN_p0.05_effect_imprinting_IN_T8_2Strand_p0.05_effect_imprinting.bed_cluster_withABSwitches
1 SP_p0.05_effect_imprinting_IN_T8_2Strand_p0.05_effect_imprinting.bed_cluster_withABSwitches
0 HT_p0.05_effect_imprinting_IN_T8_2Strand_p0.05_effect_imprinting.bed_cluster_withABSwitches
2 SK_p0.05_effect_imprinting_IN_T8_2Strand_p0.05_effect_imprinting.bed_cluster_withABSwitches
1 KD_p0.05_effect_imprinting_IN_T8_2Strand_p0.05_effect_imprinting.bed_cluster_withABSwitches
1 ST_p0.05_effect_imprinting_IN_T8_2Strand_p0.05_effect_imprinting.bed_cluster_withABSwitches
1 GI_p0.05_effect_imprinting_IN_T8_2Strand_p0.05_effect_imprinting.bed_cluster_withABSwitches
2 LV_p0.05_effect_imprinting_IN_T8_2Strand_p0.05_effect_imprinting.bed_cluster_withABSwitches
36 BN_p0.05_effect_strain_IN_T8_2Strand_p0.05_effect_strain.bed_cluster_withABSwitches
48 SP_p0.05_effect_strain_IN_T8_2Strand_p0.05_effect_strain.bed_cluster_withABSwitches
1 HT_p0.05_effect_strain_IN_T8_2Strand_p0.05_effect_strain.bed_cluster_withABSwitches
9 SK_p0.05_effect_strain_IN_T8_2Strand_p0.05_effect_strain.bed_cluster_withABSwitches
29 KD_p0.05_effect_strain_IN_T8_2Strand_p0.05_effect_strain.bed_cluster_withABSwitches
5 ST_p0.05_effect_strain_IN_T8_2Strand_p0.05_effect_strain.bed_cluster_withABSwitches
19 GI_p0.05_effect_strain_IN_T8_2Strand_p0.05_effect_strain.bed_cluster_withABSwitches
148 LV_p0.05_effect_strain_IN_T8_2Strand_p0.05_effect_strain.bed_cluster_withABSwitches
for effect in imprinting strain
do
for head in BN SP HT SK KD ST GI LV
do
bedtools intersect -wo -a <(cat ../${head}_plus_p0.05_effect_${effect}.bed ../${head}_minus_p0.05_effect_${effect}.bed |awk 'BEGIN{OFS="\t"} {print $1, $2, $3, substr($4,1,1)}') -b <(cat ../T8_2Strand_p0.05_effect_${effect}.bed_cluster |cut -f 3-)\
|awk 'BEGIN{OFS="\t"} {print $5, $6, $7, $4}' |sort | uniq |cut -f 1-3 |uniq -c \
| awk 'BEGIN{OFS="\t"} ($1==1){print $2, $3, $4}' \
> ${head}_p0.05_effect_${effect}_IN_T8_2Strand_p0.05_effect_${effect}.bed_cluster_withoutABSwitches
wc -l ${head}_p0.05_effect_${effect}_IN_T8_2Strand_p0.05_effect_${effect}.bed_cluster_withoutABSwitches
done
done
# number of domains show NO switch ($1==1) in that organ
16 BN_p0.05_effect_imprinting_IN_T8_2Strand_p0.05_effect_imprinting.bed_cluster_withoutABSwitches
6 SP_p0.05_effect_imprinting_IN_T8_2Strand_p0.05_effect_imprinting.bed_cluster_withoutABSwitches
6 HT_p0.05_effect_imprinting_IN_T8_2Strand_p0.05_effect_imprinting.bed_cluster_withoutABSwitches
10 SK_p0.05_effect_imprinting_IN_T8_2Strand_p0.05_effect_imprinting.bed_cluster_withoutABSwitches
8 KD_p0.05_effect_imprinting_IN_T8_2Strand_p0.05_effect_imprinting.bed_cluster_withoutABSwitches
8 ST_p0.05_effect_imprinting_IN_T8_2Strand_p0.05_effect_imprinting.bed_cluster_withoutABSwitches
9 GI_p0.05_effect_imprinting_IN_T8_2Strand_p0.05_effect_imprinting.bed_cluster_withoutABSwitches
11 LV_p0.05_effect_imprinting_IN_T8_2Strand_p0.05_effect_imprinting.bed_cluster_withoutABSwitches
697 BN_p0.05_effect_strain_IN_T8_2Strand_p0.05_effect_strain.bed_cluster_withoutABSwitches
976 SP_p0.05_effect_strain_IN_T8_2Strand_p0.05_effect_strain.bed_cluster_withoutABSwitches
90 HT_p0.05_effect_strain_IN_T8_2Strand_p0.05_effect_strain.bed_cluster_withoutABSwitches
273 SK_p0.05_effect_strain_IN_T8_2Strand_p0.05_effect_strain.bed_cluster_withoutABSwitches
652 KD_p0.05_effect_strain_IN_T8_2Strand_p0.05_effect_strain.bed_cluster_withoutABSwitches
338 ST_p0.05_effect_strain_IN_T8_2Strand_p0.05_effect_strain.bed_cluster_withoutABSwitches
500 GI_p0.05_effect_strain_IN_T8_2Strand_p0.05_effect_strain.bed_cluster_withoutABSwitches
1696 LV_p0.05_effect_strain_IN_T8_2Strand_p0.05_effect_strain.bed_cluster_withoutABSwitches
## Finally, identify the st domains with at least one organ with st blocks showing different allelic biases (withABSwitches).
# AND identify the im domains with at least one organ with im blocks showing different allelic biases.
for effect in strain imprinting
do
cat *_p0.05_effect_${effect}_IN_T8_2Strand_p0.05_effect_${effect}.bed_cluster_withABSwitches |sort |uniq > T8_2Strand_p0.05_effect_${effect}.bed_cluster_withABSwitches
wc -l T8_2Strand_p0.05_effect_${effect}.bed_cluster_withABSwitches
wc -l ../T8_2Strand_p0.05_effect_${effect}.bed_cluster
done
# organized in excel sheet https://www.dropbox.com/s/fqfgkuvjgnmalg0/Sup_table.xlsx?dl=0
# and perform fisher.test in R https://github.com/shaopei/F1_8Tissues/blob/master/allelic_bias_swtiches.R