I want to run HTSeq on count number of mapped mRNA reads on Human genes (GENCode GTF file). However, I have to modify this gtf file because I want to allow a search region of an offset of -200 bp upstream of each gene. I think I need to add exon of length 200bp to each gene, so, HTSeq can count the reads that overlap such regions. Do you know if there is some script (code) which can do that?
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Thank you very much @dpryan. I think I will write this code. I guess it is simple but needs more careful analysis. This is because we need to check for each gene (or transcript) if the new upstream region will not hit any upstream gene. If such case happens, then we need to shrink the upstream region accordingly. Is this right? or we let genes overlap with each other (then HTSeq will identify reads as ambiguous)
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Thanks @dpryan. I agree with you that we do not need to shrink, however, I suggested this to avoid eliminating reads from being counted by HTSeq count. Actually, I do not like the ambiguity approach in HTSeq count because it artificially changes the way the expression count is defined. I just posted a question about this.
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I agree with you if you mean that HTSeq-count is intended to generate expression matrix for detection of differentially expressed genes. Unfortunately, this is just one single applications, while, many applications need expression matrix that reflect the actual expression mechanism. Please correct me if you think this is not true and/or not accurate.
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