featureCounts with paired end option
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Varun Gupta
Jan 12, 2018, 1:48:42 PM1/12/18
to Subread
Hi,
I have a paired end rna seq data and I want to count reads over my exon. I am using the -p (isPairedEnd) option so that fragments will be counted instead of reads. I want to ask this, whether featureCounts will count
those reads where the 2nd read of the pair does not map to the exon(but farther downstream) I am interested? Will it only count it as 1 fragment if both the reads from the pair overlap the exon of interest?
Regards
Varun
I have a paired end rna seq data and I want to count reads over my exon. I am using the -p (isPairedEnd) option so that fragments will be counted instead of reads. I want to ask this, whether featureCounts will count
those reads where the 2nd read of the pair does not map to the exon(but farther downstream) I am interested? Will it only count it as 1 fragment if both the reads from the pair overlap the exon of interest?
Regards
Varun
Wei Shi
Jan 14, 2018, 5:34:48 PM1/14/18
to Subread
Hi Varun,
For your first question, yes featureCounts will count the fragment if your 2nd read does not map to the exon of interest. But please be aware that if your 2nd read maps to a different exon then featureCounts by default will not count the fragment due to multi-overlapping.
For your second question, yes featureCounts will only count it as 1 fragment.
Cheers,
Wei
For your first question, yes featureCounts will count the fragment if your 2nd read does not map to the exon of interest. But please be aware that if your 2nd read maps to a different exon then featureCounts by default will not count the fragment due to multi-overlapping.
For your second question, yes featureCounts will only count it as 1 fragment.
Cheers,
Wei
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