Does BAM input need to be sorted by name?

[Alex Lee]

Hi so I'm trying to summarize by exon using bam from STAR aligner.  However, Star output is sorted by coordinate.  Since my reads are paired-end I would like to use the -p switch, however, I'm curious if I need to resort the BAM input by name first? or will featureCounts do this automatically?  thank you! 

Alex

[Wei Shi]

No you do not need to sort your bam files. featureCounts will do that for you automatically. featureCounts processes name-sorted and location-sorted bam files at the same speed.