Quick question: is there out there a .bed (or similar) files that span over all coding regions in hg38 coordinates? I need to analyze some WGS samples
Thank you very much in advance for any help!
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wget -O - "http://ftp.ebi.ac.uk/pub/databases/gencode/Gencode_human/release_35/gencode.v35.annotation.gtf.gz" |\
gunzip -c | grep 'transcript_type "protein_coding"' |\
awk '($3=="exon") {printf("%s\t%s\t%s\n",$1,int($4)-1,$5);}' |\
sort -T . -t $'\t' -k1,1 -k2,2n | bedtools merge
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thanks so much, I was wondering, what are the regions that are filtered out between line 2 and line 3? (regions that are flagged as protein_coding but not exons?
I did and de-piped command, mine was more a theoretical question
For the future bioinformaticians who land on this page: Please note that the release 35 in no more the latest release. So you may want to update the link to the gtf.gz file in the script above. You can find out the latest release by inspecting: http://ftp.ebi.ac.uk/pub/databases/gencode/Gencode_human/. For example, the current release (as of May 2022) is release 40, thus the link is: http://ftp.ebi.ac.uk/pub/databases/gencode/Gencode_human/release_40/gencode.v40.annotation.gtf.gz.
By the way, the coordinates are on the human reference genome: hg38 (i.e.GRCh38).
unrelated to the original question.
GTF is 1-based while BED is 0-based. See:
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You could download the hg38 GTF file from GENCODE and extract relevant columns and records from it.