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Old 12-11-2013, 12:49 PM   #1
11xinqi
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Location: china

Join Date: Mar 2011
Posts: 31
Default Htseq-count problem

Hi all

I met a problem with htseq-count. I use the command - htseq-count -s no N4sn.sam merged.gtf >N4.count- to get the reads number for features. Then I checked for a specific gene with gene id (XLOC_055054). the command used is grep "XLOC_055054" N4.count. the result shows that reads count is 0 for this gene. But that is wrong. I can see so many reads mapped to this gene from IGV, and also I got the annotation (nob.gtf) only containing this one gene and rerun -htseq-count -s no N4sn.sam nob.gtf >N41.count. the result shows that XLOC_055054 3853. Anyone can tell me why I get the difference result?
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