bowtie2: Print only Alignment Summary?

Question

[jer364]

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!

[GenoMax]

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

Answer 1

[ATpoint]

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.

[jer364]

Thank you! This worked!