[BioC] how to get the exon count by using htseq-count

Simon Anders anders at embl.de
Tue Mar 19 14:10:56 CET 2013


On 19/03/13 10:45, Hu Fuyan [guest] wrote:
> How to get the exon count by using htseq-count?
> My script is:
> python -m HTSeq.scripts.count -m intersection-strict --stranded=no -t exon -i exon_id  accepted_hits_name.sorted.sam Homo_sapiens.GRCh37.70_new.gtf>outfile_htseqcount_exon

You should not use htseq-count for this purpose. Rather, use the Python 
scripts dexseq-prepare.py and dexseq-count.py.

For more information, please see the last section of the DEXSeq vignette 
and the relevant sections in the vignette of the pasilla package.

If this does not help, please ask again.


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