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identifying 3'utrs for multiple transcripts of genes from a summarized experiment.

Hello all,

I have a summarized experiment containing salmon-predicted transcript counts. I am primarily interested in getting the sequence for the 3'utrs for all a gene's various alternative transcripts that have a distinct 3'utr. Im wondering what would be the most efficient way of getting this data. Previously, when working on gene counts, I used the biomart mane select option to download a single representative 3'utr, but I am unsure of how to get transcript-specific 3'utrs from biomart, if that is even possible. Alternatively, is there another database you would recommend? Please let me know your thoughts.

Thanks!

biomart transcriptome utr
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written by RNAseqer RNAseqer

1 answer

get the exons from the protein-coding genes and remove the coordinates of the CDS.

bedtools subtract \
     -a <(wget -qO - "https://ftp.ebi.ac.uk/pub/databases/gencode/Gencode_human/release_47/gencode.v47.annotation.gtf.gz" | gunzip -c | awk -F '\t' '($3=="exon" && $9 ~ /protein_coding/) {printf("%s\t%d\t%s\n",$1,int($4)-1,$5);}' | LC_ALL=C sort -T . -t $'\t' -k1,1 -k2,2n ) \
   -b <(wget -qO - "https://ftp.ebi.ac.uk/pub/databases/gencode/Gencode_human/release_47/gencode.v47.annotation.gtf.gz" | gunzip -c | awk -F '\t' '($3=="CDS" && $9 ~ /protein_coding/) {printf("%s\t%d\t%s\n",$1,int($4)-1,$5);}' | LC_ALL=C sort -T . -t $'\t' -k1,1 -k2,2n ) |\
 LC_ALL=C sort -T . -t $'\t' -k1,1 -k2,2n | bedtools merge
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written by Pierre Lindenbaum Pierre Lindenbaum

Thanks! This worked like a charm. I appreciate the help.

• 0 views • link
written by RNAseqer RNAseqer

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