Run htseq-count with multiple sam files?
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8.5 years ago

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,

RNA-Seq htseq-count • 7.5k views
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Use featureCounts much faster than HTseq and supports multiple samples.

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8.5 years ago
GenoMax 148k

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.

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8.5 years ago
michael.ante ★ 3.9k

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

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6.5 years ago
Arindam Ghosh ▴ 530

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

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6.5 years ago

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

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