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!
You may be able to get that by not providing an output file name for the alignments.
By default bowtie2 prints to stdout which you could redirect to /dev/null like
bowtie2 (...) > /dev/null.
bowtie2 (...) > /dev/null
The summary probably gets printed to stderr. I would test that first on a few reads to confirm this works.
Thank you! This worked!
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