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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.

  • #2
    I solved this by choosing the appropriate option, -s -i -t.
    Sorry, but I have no idea about how to delete my post.
    Last edited by syintel87; 01-06-2013, 05:17 PM.

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