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Old 04-06-2014, 11:56 PM   #3
Location: Germany

Join Date: Dec 2013
Posts: 16

That's very concise and informative. Thank you for the answer !

However, one more thing troubles me, I have an Ensembl GRCm38 .gtf file that contains in 3rd column values such as exon, CDS, start_codon, stop_codon, but no "gene". Since I want to use the .gtf file for HTseq counting of reads based on their overall mapping to genes, I thought I should use the -t gene option. Otherwise the default -t exon would count the multi-exon reads twice into same gene, like the DEXseq counting script, right ? Or maybe the -t exon option is fine for preparing count tables for DESeq ?

Last edited by kajot; 04-07-2014 at 12:18 AM.
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