Merge featurecounts lists

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2.5 years ago

imaparna27 ▴ 20

I have a very large RNA-Seq sample size (n=100), so while performing quantification through featurecounts, Rstudio crashed. So, I decided to perform the analysis in chunks (n=20 bam files). Hence, I generated 5 lists through featurecounts (fc1,fc2....). Now I tried to merge all these lists in one list fc, but the dimension of fc is list of 20 (ideally should have been- list of 4=> annotation;counts;target;stats).

Functions I used to merge lists- c(fc1,fc2), mapply(fc1,fc2), rbind(fc1,fc2), Map(list,fc1,fc2).

What mistakes I might be doing? Any alternative for merging lists so that I get only one list (ideal list of 4)? Any other way so that I can process all files at once in R?

merge-lists featurecounts Rstudio dimension • 915 views

ADD COMMENT • link 2.5 years ago by imaparna27 ▴ 20

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I would suggest running featureCounts on the command line and using multiple threads (depending on the local machine you are using). If you have access to a server, even better. That should probably avoid it from crashing and, this way, directly obtaining the full count matrix.

ADD REPLY • link 2.5 years ago by Marco Pannone ▴ 810

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I was already using 20 threads in Rstudio. Although, I didn't realise command line option at first. Thanks a lot.

ADD REPLY • link 2.5 years ago by imaparna27 ▴ 20

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