Question: bowtie2: Print only Alignment Summary?
gravatar for jer364
15 days ago by
jer3640 wrote:

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!

rna-seq alignment • 131 views
ADD COMMENTlink written 15 days ago by jer3640

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

ADD REPLYlink written 15 days ago by genomax92k
gravatar for ATpoint
14 days ago by
ATpoint42k wrote:

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.

ADD COMMENTlink written 14 days ago by ATpoint42k

Thank you! This worked!

ADD REPLYlink written 7 days ago by jer3640
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