written 26 days ago by
laurah ondari
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7
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2
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610
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5
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110
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110
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4
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110
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Comment: Clarification on counting in Rsubread (featureCounts)
by
Luca
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Thanks to both of you for your helpful suggestions.
The counting was already strand-specific at both the exon and gene levels. I resolved …
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Have you told featureCounts to do strand-specific counting?
As pointed out by Frances Turner, you can lose reads if they overlap the gene …
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You should look at the summary files produced by feature counts. This gives a breakdown of what happened to reads that were not assigned. Y…
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Just played with this a bit and I think it comes down to not having a fixed seed before running the leiden thingy. Same goes for PCA and UM…
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The most obvious thing that comes to mind is the RNG seed. `cluster_leiden()` does some random number generation, somewhere deep in the **i…
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