I solved this by choosing the appropriate option, -s -i -t.
Sorry, but I have no idea about how to delete my post.
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interpretation of output from HTSeq
I ran the four commands below.
python -m HTSeq.scripts.count accepted_hits.sam Mh.gtf > count.txt
samtools view accepted_hits.bam | python -m HTSeq.scripts.count - Mh.gtf > count.txt
samtools view accepted_hits.bam | python -m HTSeq.scripts.count -m intersection-strict - Mh.gtf > count.txt
samtools view accepted_hits.bam | python -m HTSeq.scripts.count -m intersection-nonempty - Mh.gtf > count.txt
However, all of the outputs show the same result:
no_feature 0
ambiguous 0
too_low_aQual 0
not_aligned 0
alignment_not_unique 409168
With this result, I don't think I can move to the next step, DESeq.
How could I make interpretation on this? Would you see what is wrong with my commands or result and what whould be fixed?
Thank you in advance.Last edited by syintel87; 01-06-2013, 01:56 PM.
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