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BioGen 09-21-2017 12:34 PM

HT-Seq counts questions
Hi everyone,

I want to analyse my .bam files (sorted and indexed), that have been mapped by someone else before.

These are as this:
- sample.merged.mdup.forward.bam
- sample.merged.mdup.reverse.bam

when looking for ht-seq counts tutorials, inputs were only one bam (reverse+forward) and the gff.

#1 What I wanted to know is : is it possible to use the sample.merged.mdup.forward.bam
and the sample.merged.mdup.reverse, as my inputs (+gff)?

#2 If yes, how does the script line looks (i'm beginner in computational analysis :/ )

#3 If not, does it need to merge the forward and the reverse together?

#4 What does "mdup" mean?

Many thanks in advance :)

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