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syintel87 06-17-2013 01:18 PM

[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.

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