iosonofabio
commented
6 years ago Sorry which are the 10 exons?
On December 19, 2017 7:19:21 AM PST, Komal Rathi notifications@github.com wrote:
Hi,
I have a bunch of samples from various tumor types in which I want to get the exon level expression of the gene IDO1. My aim is not to do any differential expression of any sort because there are no control samples. I prepared the gencode v23 gtf to gff using the following command:
python2.7 dexseq_prepare_annotation.py gencode.v23.annotation.gtf gencode.v23.annotation.gffThis gave me 33 exonic parts for the gene IDO1:
chr8 dexseq_prepare_annotation.py aggregate_gene 39902275 39928444 . + . gene_id "ENSG00000131203.12" chr8 dexseq_prepare_annotation.py exonic_part 39902275 39902370 . + . transcripts "ENST00000518804.5"; exonic_part_number "001"; gene_id "ENSG00000131203.12" chr8 dexseq_prepare_annotation.py exonic_part 39902371 39902374 . + . transcripts "ENST00000518804.5+ENST00000519154.5"; exonic_part_number "002"; gene_id "ENSG00000131203.12" chr8 dexseq_prepare_annotation.py exonic_part 39902375 39902379 . + . transcripts "ENST00000518804.5+ENST00000522495.5+ENST00000519154.5"; exonic_part_number "003"; gene_id "ENSG00000131203.12" chr8 dexseq_prepare_annotation.py exonic_part 39902380 39902448 . + . transcripts "ENST00000518804.5+ENST00000522840.1+ENST00000522495.5+ENST00000519154.5"; exonic_part_number "004"; gene_id "ENSG00000131203.12" chr8 dexseq_prepare_annotation.py exonic_part 39908989 39909030 . + . transcripts "ENST00000522840.1"; exonic_part_number "005"; gene_id "ENSG00000131203.12" chr8 dexseq_prepare_annotation.py exonic_part 39909179 39909348 . + . transcripts "ENST00000518804.5+ENST00000522840.1"; exonic_part_number "006"; gene_id "ENSG00000131203.12" chr8 dexseq_prepare_annotation.py exonic_part 39913001 39913148 . + . transcripts "ENST00000522495.5"; exonic_part_number "007"; gene_id "ENSG00000131203.12" chr8 dexseq_prepare_annotation.py exonic_part 39913284 39913402 . + . transcripts "ENST00000518237.5"; exonic_part_number "008"; gene_id "ENSG00000131203.12" chr8 dexseq_prepare_annotation.py exonic_part 39913403 39913773 . + . transcripts "ENST00000518237.5+ENST00000519154.5"; exonic_part_number "009"; gene_id "ENSG00000131203.12" chr8 dexseq_prepare_annotation.py exonic_part 39913774 39913868 . + . transcripts "ENST00000518237.5+ENST00000522840.1+ENST00000519154.5"; exonic_part_number "010"; gene_id "ENSG00000131203.12" chr8 dexseq_prepare_annotation.py exonic_part 39913869 39913888 . + . transcripts "ENST00000518237.5+ENST00000522840.1+ENST00000253513.11+ENST00000519154.5"; exonic_part_number "011"; gene_id "ENSG00000131203.12" chr8 dexseq_prepare_annotation.py exonic_part 39913889 39914009 . + . transcripts "ENST00000518804.5+ENST00000522495.5+ENST00000519154.5+ENST00000518237.5+ENST00000522840.1+ENST00000253513.11"; exonic_part_number "012"; gene_id "ENSG00000131203.12" chr8 dexseq_prepare_annotation.py exonic_part 39917875 39917884 . + . transcripts "ENST00000518804.5+ENST00000522495.5+ENST00000519154.5+ENST00000518237.5+ENST00000522840.1+ENST00000253513.11"; exonic_part_number "013"; gene_id "ENSG00000131203.12" chr8 dexseq_prepare_annotation.py exonic_part 39917885 39917929 . + . transcripts "ENST00000518237.5+ENST00000522495.5+ENST00000519154.5+ENST00000518804.5+ENST00000521636.1+ENST00000522840.1+ENST00000253513.11"; exonic_part_number "014"; gene_id "ENSG00000131203.12" chr8 dexseq_prepare_annotation.py exonic_part 39917930 39917970 . + . transcripts "ENST00000518804.5+ENST00000522495.5+ENST00000519154.5+ENST00000518237.5+ENST00000521636.1+ENST00000253513.11"; exonic_part_number "015"; gene_id "ENSG00000131203.12" chr8 dexseq_prepare_annotation.py exonic_part 39918088 39918138 . + . transcripts "ENST00000518804.5+ENST00000522495.5+ENST00000519154.5+ENST00000518237.5+ENST00000521636.1+ENST00000253513.11"; exonic_part_number "016"; gene_id "ENSG00000131203.12" chr8 dexseq_prepare_annotation.py exonic_part 39918139 39918207 . + . transcripts "ENST00000518237.5+ENST00000521636.1+ENST00000522495.5+ENST00000519154.5+ENST00000253513.11"; exonic_part_number "017"; gene_id "ENSG00000131203.12" chr8 dexseq_prepare_annotation.py exonic_part 39918815 39918933 . + . transcripts "ENST00000518237.5+ENST00000521636.1+ENST00000522495.5+ENST00000519154.5+ENST00000253513.11"; exonic_part_number "018"; gene_id "ENSG00000131203.12" chr8 dexseq_prepare_annotation.py exonic_part 39918934 39918944 . + . transcripts "ENST00000253513.11"; exonic_part_number "019"; gene_id "ENSG00000131203.12" chr8 dexseq_prepare_annotation.py exonic_part 39920100 39920114 . + . transcripts "ENST00000518237.5+ENST00000521636.1+ENST00000522495.5+ENST00000519154.5"; exonic_part_number "020"; gene_id "ENSG00000131203.12" chr8 dexseq_prepare_annotation.py exonic_part 39922552 39922651 . + . transcripts "ENST00000521480.1+ENST00000522495.5+ENST00000519154.5+ENST00000518237.5+ENST00000521636.1+ENST00000253513.11"; exonic_part_number "021"; gene_id "ENSG00000131203.12" chr8 dexseq_prepare_annotation.py exonic_part 39922652 39922654 . + . transcripts "ENST00000521636.1+ENST00000519154.5"; exonic_part_number "022"; gene_id "ENSG00000131203.12" chr8 dexseq_prepare_annotation.py exonic_part 39922655 39922911 . + . transcripts "ENST00000521636.1"; exonic_part_number "023"; gene_id "ENSG00000131203.12" chr8 dexseq_prepare_annotation.py exonic_part 39923469 39923586 . + . transcripts "ENST00000518237.5+ENST00000521480.1+ENST00000522495.5+ENST00000253513.11"; exonic_part_number "024"; gene_id "ENSG00000131203.12" chr8 dexseq_prepare_annotation.py exonic_part 39923587 39923590 . + . transcripts "ENST00000521480.1+ENST00000253513.11"; exonic_part_number "025"; gene_id "ENSG00000131203.12" chr8 dexseq_prepare_annotation.py exonic_part 39923591 39923931 . + . transcripts "ENST00000521480.1"; exonic_part_number "026"; gene_id "ENSG00000131203.12" chr8 dexseq_prepare_annotation.py exonic_part 39924720 39924720 . + . transcripts "ENST00000523779.1"; exonic_part_number "027"; gene_id "ENSG00000131203.12" chr8 dexseq_prepare_annotation.py exonic_part 39924721 39924772 . + . transcripts "ENST00000518237.5+ENST00000523779.1+ENST00000522495.5+ENST00000253513.11"; exonic_part_number "028"; gene_id "ENSG00000131203.12" chr8 dexseq_prepare_annotation.py exonic_part 39925223 39925371 . + . transcripts "ENST00000518237.5+ENST00000523779.1+ENST00000522495.5+ENST00000253513.11"; exonic_part_number "029"; gene_id "ENSG00000131203.12" chr8 dexseq_prepare_annotation.py exonic_part 39927830 39928138 . + . transcripts "ENST00000518237.5+ENST00000523779.1+ENST00000522495.5+ENST00000253513.11"; exonic_part_number "030"; gene_id "ENSG00000131203.12" chr8 dexseq_prepare_annotation.py exonic_part 39928139 39928426 . + . transcripts "ENST00000518237.5+ENST00000522495.5+ENST00000253513.11"; exonic_part_number "031"; gene_id "ENSG00000131203.12" chr8 dexseq_prepare_annotation.py exonic_part 39928427 39928431 . + . transcripts "ENST00000518237.5+ENST00000253513.11"; exonic_part_number "032"; gene_id "ENSG00000131203.12" chr8 dexseq_prepare_annotation.py exonic_part 39928432 39928444 . + . transcripts "ENST00000253513.11"; exonic_part_number "033"; gene_id "ENSG00000131203.12"Then, I ran dexseq_count.py like this:
python2.7 dexseq_count.py -f bam -p yes -r pos -s no gencode.v23.annotation.gff sample1_Aligned.out.sorted.bam output.txtAnd these are the corresponding counts for all 33 exonic parts of IDO1:
ENSG00000131203.12:001 1 ENSG00000131203.12:002 1 ENSG00000131203.12:003 1 ENSG00000131203.12:004 3 ENSG00000131203.12:005 0 ENSG00000131203.12:006 0 ENSG00000131203.12:007 0 ENSG00000131203.12:008 0 ENSG00000131203.12:009 0 ENSG00000131203.12:010 2 ENSG00000131203.12:011 2 ENSG00000131203.12:012 3 ENSG00000131203.12:013 1 ENSG00000131203.12:014 1 ENSG00000131203.12:015 1 ENSG00000131203.12:016 1 ENSG00000131203.12:017 1 ENSG00000131203.12:018 0 ENSG00000131203.12:019 0 ENSG00000131203.12:020 2 ENSG00000131203.12:021 6 ENSG00000131203.12:022 1 ENSG00000131203.12:023 1 ENSG00000131203.12:024 4 ENSG00000131203.12:025 0 ENSG00000131203.12:026 0 ENSG00000131203.12:027 0 ENSG00000131203.12:028 3 ENSG00000131203.12:029 4 ENSG00000131203.12:030 34 ENSG00000131203.12:031 29 ENSG00000131203.12:032 2 ENSG00000131203.12:033 2However, when I looked in UCSC there are only 10 IDO1 exons. Because I am only interested in getting the exon level expression and no differential expression I am wondering if there is a way to modify the gff to just keep the actual exon coordinates? Or is there a way to merge these 33 exons to get counts for the 10 exons? Please advise.
Thanks!
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komalsrathi
Hi,
I have a bunch of samples from various tumor types in which I want to get the exon level expression of the gene IDO1. My aim is not to do any differential expression of any sort because there are no control samples. I prepared the gencode v23 gtf to gff using the following command:
This gave me 33 exonic parts for the gene IDO1:
Then, I ran dexseq_count.py like this:
And these are the corresponding counts for all 33 exonic parts of IDO1:
However, when I looked in UCSC there are only 10 IDO1 exons. Because I am only interested in getting the exon level expression and no differential expression I am wondering if there is a way to modify the gff to just keep the actual exon coordinates? Or is there a way to merge these 33 exons to get counts for the 10 exons? Please advise.
Thanks!