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bowtie2: Print only Alignment Summary?

I'm assembling transcriptomes and am trying to map my reads back to my contigs using bowtie2. Is there a way to only print the summary statistics or ignore alignment information? Otherwise summary file is hundreds of gigs. Thanks for any help!

alignment rna-seq
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written by jer364 • jer364

You may be able to get that by not providing an output file name for the alignments.

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written by GenoMax GenoMax

1 answer

By default bowtie2 prints to stdout which you could redirect to /dev/null like

bowtie2 (...) > /dev/null.

The summary probably gets printed to stderr. I would test that first on a few reads to confirm this works.

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written by ATpoint ATpoint

Thank you! This worked!

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written by jer364 • jer364

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