How to get unquantified reads with featurecounts
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5.5 years ago
Chynoki • 0

Hi there, I'm using featurecounts and I'm wondering if their is a way to get all reads which where not quantified by this software (i.e unassigned reads). I didn't find this option in the Subread documentation.

If it's not possible maybe someone can help me. I try to make a pipeline to analyse smallRNA-seq data. I want to quantify miRNA first on my dataset and then try to quantify other smallRNA (piRNA, snoRNa,...) but I think it would induce some biais if reads quantified as miRNA are still present in the dataset when I'll quantify other smallRNA. Do you think I'm right or not?

Thank you

quantification • 883 views
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