This function helps you to locate motifs on the reference fasta sequences provided by the user. As a prerequisite user have to provide the list of motifs and reference fasta sequence. User have to mention if he wants to display percentile location i.e. in case of ChIPSeq peaks when the binding site have variable lengths displaying percent position makes more sense. Or you can just plot the start of the motif on the sequence. This function takes into account the reverse complement of the motif while finding the motif so no need to worry about the motifs on complementary strands.
Input files
1. fastaSequence file
>GeneA
GTGCAACGCGTATAAACCTTTGGGCCTCTCTCACGATGAATAGGGGCAGTAGCATTACACTCTGGCATAACAATAGGGCCCTGGCAATAGGGCTCTGGCAATAGGGCTCTGGCAATAGACTGTGGGAGGGCCATACTG
>GeneB
TAGAAGAAAAAAAGACAAGCAAAACAAAATCACACAACACATAATCAAAAAGCATTACACTCTGGCATAACAATAGGGCCCTGGCAATAGGGCTCTGGCAATAGGGCTCTGGCAATAGACTGTGGGAGGGCCATACTG
2. mymotifs (can be copied from clipboard)
TCAATAGGGGATT
TGAATAGGGGC
ACAATAGGGCC
GCAATAGGGCT
GCAATAGGGCT
Run the function as:
motif_location_on_sequence(fastaSequence, mymotifs,"outfile",x = "start")
- outfile_GenesWithMotifs.txt
- Motif location visualisation
This function helps to visualise motif distribution in the binding site of ChIP signal. As a a input provide list of motifs, genome fasta sequence, summits bedfile and flanking basepair from summits. Please mention which if the reverse complement of the given motifs is to be considered, works for DNA nucleotides only (A,T,G,C,N)
Input files
1. genome_fasta
>chrA
GTGCAACGCGTATAAACCTTTGGGCCTCTCTCACGATGAATAGGGGCAGTAGCATTACACTCTGGCATAACAATAGGGCCCTGGCAATAGGGCTCTGGCAATAGGGCTCTGGCAATAGACTGTGGGAGGGCCATACTG
>chrB
TAGAAGAAAAAAAGACAAGCAAAACAAAATCACACAACACATAATCAAAAAGCATTACACTCTGGCATAACAATAGGGCCCTGGCAATAGGGCTCTGGCAATAGGGCTCTGGCAATAGACTGTGGGAGGGCCATACTG
2. mymotifs (can be copied from clipboard)
TCAATAGGGGATT
TGAATAGGGGC
ACAATAGGGCC
GCAATAGGGCT
GCAATAGGGCT
3. macs2_summit_file
ChrA 222666 222667 A_narrow_peak_1 97.17213
ChrB 519643 519644 A_narrow_peak_2 12.13631
ChrA 619813 619814 A_narrow_peak_3 49.07928
ChrY 860772 860773 A_narrow_peak_4 24.225
ChrA 892756 892757 A_narrow_peak_5 219.14851
ChrB 897564 897565 A_narrow_peak_6 17.06805
ChrA 1281067 1281068 A_narrow_peak_7 212.36813
ChrY 1585030 1585031 A_narrow_peak_8 14.14571
4. flank_from_summit = 100
5. motif_revComplement="TRUE" (By default it is false)
Run the function as:
motif_distirbution_from_summits(macs2_summit_file,genome_fasta,mymotifs,flank_from_summit = 100, motif_revComplement="TRUE")
- Motif distibution visualisation
