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Old 06-09-2013, 03:04 PM   #41
Baoqing
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Location: Texas

Join Date: Jan 2013
Posts: 24
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sorry, just start to pick up the python, any reminder message freak me out.

Just set up the path right for htseq-count

then run it with my bam files:
samtools view accepted_hits.bam | htseq-count - gene.gtf > counts.txt

While the program was running, there was a warning "claimed to have an aligned mate which could be found. (Is the sam file properly sorted?)

Does this warning "complaining that my file is not pair mated, or do i have to add other arguments for this line to run?

Thanks a lot for your help!

Best,

Last edited by Baoqing; 06-09-2013 at 03:56 PM.
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