Featurecounts

Question

[biology_inform]

Can I use directly unsorted Bam files in feature counts (sequences are paired end)?

Also I couldn't reach the manual of featurecounts. How can I reach it?

Answer 1

[biofalconch]

1) Yes, you can use an unsorted bam file as featureCounts sorts it.

2) featureCounts is part of subread, you can find the documentation here (page 32 of the document)

[ATpoint]

In fact you can use sorted BAM files as featureCounts sorts it. Unsorted require no sorting as the paired-end data would already be grouped.

[biology_inform]

thanks to both of you!