Run htseq-count with multiple sam files?

Question

[lynne.m.a.harris]

Can one only run one sam file at a time? Or is there a way to run multiple sams in one command line? I have 27 sam files.

Thanks,

[Arup Ghosh]

Use featureCounts much faster than HTseq and supports multiple samples.

Answer 1

[GenoMax]

featureCounts will allow you to use multiple files at the same time and will generate a count matrix in one step. It is also much faster and will sort files automatically, if needed.

Answer 2

[michael.ante]

You can use GNU parallel to run multiple instances. See this tutorial for further information.

Answer 3

[Arindam Ghosh]

A small perl script will do the job and then use R to combine results into one file.

Answer 4

[Kristoffer Vitting-Seerup]

Why not quantify with Salmon - will give you much better gene level estimats (according to amongst other this)