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Old 06-17-2013, 02:18 PM   #1
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Join Date: Dec 2012
Posts: 81
Default [HTSeq-Count] How are reads counted?

I have questions about how htseq-count software counts reads.

What I wonder is...
When are reads not counted but ignored from counting?
When are reads counted as 1?
How many mapped reads are counted as some number?

Would you please give me tips about these?
Thank you in advance.

Last edited by syintel87; 06-17-2013 at 02:22 PM.
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