Question

Long-read mode in featureCounts

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mmisak • 0

@6a9a6067

Last seen 13 months ago

Germany

Hello, I have a rather simple question: featureCounts has a long-read mode ("isLongRead" parameter). How does this parameter affect the counting behavior of featureCounts?

Thank you

Rsubread LongRead • 1.1k views

ADD COMMENT • link 13 months ago mmisak • 0

score 2 · Answer 1 · 2023-10-14

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Wei Shi ★ 3.6k

@wei-shi-2183

Last seen 3 months ago

Australia/Melbourne/Olivia Newton-John …

It doesn't really change the behaviour of featureCounts. It just instructs featureCounts to consider more exons and exon junctions in a long read.

ADD COMMENT • link 13 months ago Wei Shi ★ 3.6k

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Thank you for your reply.

So does that mean, it impacts only the behavior of the "juncCounts" (-J) parameter and not at all the counting on meta-feature (i.e. gene) level or anything else? If so, to how many junctions is featureCounts limited in normal (i.e. short read) mode and how many are supported when setting the "isLongRead" (-L) parameter? I tried to find this in the user's guide but couldn't find any information on it.

ADD REPLY • link 13 months ago mmisak • 0