Featurecounts countmatrix creation
Hello,
I have 15 BAM files, with 5 belonging to each of the control, treatment1, and treatment2 groups. I am wondering whether I should use all of the BAM files at once in the featureCounts command to create single count file for downstream analysis or if I should perform featureCounts on the individual BAM files separately. I am not sure if using all of the BAM files at once could cause any issues in downstream analysis such as differential expression analysis.
Thank you in advance!
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rpolicastro
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Vikram •
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Vikram •
1 answer
Running them all together is fine. It just puts all the counts into one file so it's slightly easier to import into e.g. R.
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