library size calculation using DESeq1/2

[aburkhardt]

Hello,
I would like to know if the lines at the end of the HTSeq file (which includes _no_feature, _ambiguous, _too_low_aQual, _not_aligned, and alignment_not_unique) are included in the library size estimations for either DESeq or DESeq2. I have a sample with a higher number of reads under the "_ambiguous" that the others and want to make sure that it is not affecting my other calculations.
Thank you.

[Michael Love]

These counts are not included in the dds. You can check with:

tail(counts(dds))

And as they are not in the count matrix, they will not influence the library size estimates.