Hi folks!
Im using HTSeq to count reads and so far i used the default option --type=exon.
However, it would be useful for me to distinguish reads mapping in UTRs and those mapping in exons that are part of the coding sequence.
Do you think i could use something like --type=UTR and then for each gene_id subtract these from the reads i count with the type=exon method?
To my understanding "exon" here does not necessarily signify a coding portion of the gene. I expect that some sections of UTRs could still be counted under the default exon method.
Or how would you go about distinguishing counts between coding sequence and UTR regions?
Im using HTSeq to count reads and so far i used the default option --type=exon.
However, it would be useful for me to distinguish reads mapping in UTRs and those mapping in exons that are part of the coding sequence.
Do you think i could use something like --type=UTR and then for each gene_id subtract these from the reads i count with the type=exon method?
To my understanding "exon" here does not necessarily signify a coding portion of the gene. I expect that some sections of UTRs could still be counted under the default exon method.
Or how would you go about distinguishing counts between coding sequence and UTR regions?
Comment