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data_sources.txt
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# circRNA databases
circAtlas2.0_June2019_human_hg19_circRNA.0-based.bed -> download from circatlas / skip for release
CIRCpedia_v2_June2019_human_hg19_All_circRNA.unique.bed -> download from circatlas / skip for release
hsa_circRNA_complete.hg19.unique.sort.length.bed -> This is circbase
# primary genome files
hg19.chrom.sizes -> standard genome file -> https://hgdownload.soe.ucsc.edu/goldenPath/hg38/bigZips/
hg19.fa -> standard genome file -> https://hgdownload.soe.ucsc.edu/goldenPath/hg38/bigZips/
hg19.fa.fai -> standard genome file -> build with faidx
# from UCSC browser, postprocessed refFlat files (base file download):
https://genome.ucsc.edu/cgi-bin/hgTables?jsh_pageVertPos=0&clade=mammal&org=Human&db=hg38&hgta_group=allTables&hgta_track=hg38&hgta_table=refFlat&hgta_regionType=genome&hgta_outputType=primaryTable&boolshad.sendToGalaxy=0&boolshad.sendToGreat=0&hgta_outFileName=foo.gz&hgta_outSep=tab&hgta_compressType=gzip&hgta_doTopSubmit=Get+output
Human_refFlat_exon_hg19_Oct2018.merge.bed -> DONE
Human_refFlat_exon_hg19_Oct2018.sort.bed -> DONE
Human_refFlat_hg19_Oct2018.unique.merge.bed -> DONE
# GENCODE: https://www.gencodegenes.org/human/release_37lift37.html (base file download)
gencode.v37lift37.annotation.gffread.exon.bed -> DONE
-> via script
gencode.v37lift37.annotation.gffread.exon.merge.bed -> DONE
-> via script
hg19_ucsc_Intron_Gencode_V34lift37.bed (file ready after download):
https://genome.ucsc.edu/cgi-bin/hgTables?clade=mammal&org=Human&db=hg19&hgta_group=genes&hgta_track=wgEncodeGencodeV34lift37&hgta_table=0&hgta_regionType=genome&hgta_outFileName=test.gz.gz&hgta_ctVis=pack&hgta_ctUrl=&fbUpBases=200&fbExonBases=0&fbQual=intron&fbIntronBases=0&fbDownBases=200&hgta_doGetBed=get+BED&hgta_compressType=gzip
UCSC-EST-exons_hg19_09-2018.bed (file ready after download):
https://genome.ucsc.edu/cgi-bin/hgTables?hgta_ctName=tb_all_est&hgta_ctUrl=&fbUpBases=200&fbQual=exon&fbExonBases=0&fbIntronBases=0&fbDownBases=200&hgta_doGetBed=get+BED&clade=mammal&org=Human&db=hg19&hgta_group=allTracks&hgta_track=intronEst&hgta_table=all_est&hgta_regionType=genome&hgta_outputType=bed&hgta_outFileName=test3.gz&hgta_compressType=gzip