#30 Counts on single and paired ends reads merged bam file

[amuller]

Dear all,
We have made experiments either paired-end AND single-end on the same sample. Next, the 2 corresponding BAM files has been merged, making some difficulties for htseq-count ('pair_alignments' needs a sequence of paired-end alignments).
A fix is to use the 2 UNmerged BAM files with htseq-count separately, followed by a merge of the results files (simply summing the counts paired-end + single-end).
Is that approach healthy and recommended?
Best regards.
PS: HTSeq rocks!