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Subread FeatureCounts for Exon level quantification: Length estimate for Exons as low as 1 base-pair
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Answer: RSubread output significantly different from bash Subread output
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Gordon Smyth
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The difference (as ATpoint has correctly pointed out) is that Rsubread::featureCounts counts multi-mapping reads by default whereas the com…
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I would check the rank of your model matrix, and perhaps meet with a local statistician who can help you create an appropriate design matri…
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Agreed. I'll add that with small sample size, a covariate can explain some fraction of expression variation even under the null.
Comment: RSubread output significantly different from bash Subread output
by
Aimee
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Thank you! I will try rerunning with that parameter and see if it fixes the discrepancy! I'll report back.
Update: This completely resolve…
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The R version counts multimappers (countMultiMappingReads is TRUE by default) while the command line version does not. It's beyond me why t…
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