In the count files from HTSeq there are a few lines at the end:
__no_feature
__ambiguous
__too_low_aQual
__not_aligned
__alignment_not_unique
Should these lines be removed before loading into DESeq? I seem to get slightly different normalized counts when I create a count data set using newCountDataSet on a count table or newCountDataSetFromHTSeqCount directly on the HTSeq counts. Could this be due to these last lines?
__no_feature
__ambiguous
__too_low_aQual
__not_aligned
__alignment_not_unique
Should these lines be removed before loading into DESeq? I seem to get slightly different normalized counts when I create a count data set using newCountDataSet on a count table or newCountDataSetFromHTSeqCount directly on the HTSeq counts. Could this be due to these last lines?
Comment