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Hi,
I have a question on the matching counts in htseq-count for paired end data: i have paired-end sequencing data, not strand-specific. For strand-specific paired end sequencing data i found in the htseq documentation the following:
--stranded yes: For paired-end reads, the first read has to be on the same strand and the second read on the opposite strand. For stranded=reverse, these rules are reversed.
I would like to know now if in case of paired end, not strand-specific data the same applies (regardless the strand) meaning that: do we have only a count if one read maps on one strand and the second to the complementary strand (e.g. first strand on forward and second on reverse or vice versa) within the same feature? Do only properly paired read pairs count?
Thank you very much!
Karin
I have a question on the matching counts in htseq-count for paired end data: i have paired-end sequencing data, not strand-specific. For strand-specific paired end sequencing data i found in the htseq documentation the following:
--stranded yes: For paired-end reads, the first read has to be on the same strand and the second read on the opposite strand. For stranded=reverse, these rules are reversed.
I would like to know now if in case of paired end, not strand-specific data the same applies (regardless the strand) meaning that: do we have only a count if one read maps on one strand and the second to the complementary strand (e.g. first strand on forward and second on reverse or vice versa) within the same feature? Do only properly paired read pairs count?
Thank you very much!
Karin