Entering edit mode
4.3 years ago
felipead66
▴
110
I apologize for the silly question, but how do I find the library size of rna seq data if I have the count table? The count table was created using htseq.
Is it just the sum of the counts of genes?
the problem is not the question, but the term vague "library size". It depends on what you want to do with the estimate. For diff expression normalisation one normally uses the sum of counts in genes. If you mean the count of all the reads that came out of the sequencer for your library? Then depending on the preprocessing (e.g. adapter trimming, removal of small fragments, removal of contaminants) you might not have all the needed info. Then the best approximation you have is sum of count in genes + the sum of the last 4? rows which is the unassigned or ambigous reads.
The actual "usable" (and therefore meaningful) library size that goes into normalization and DEG analysis is the column sum for each sample considering the genes you quantified against excluding rRNAs imho.