1
$\begingroup$

BowTie2 puts out summary info to the terminal but doesn't allow me to save each to a separate file. How can I go about saving the output of BowTie2 so that MultiQC can read it and create a website from it?

$\endgroup$
1
$\begingroup$

After trying on my own this is the solution I came up with. My solution was to use a pipe of the stderr into a new file.

bowtie2 --local --threads 4 -x reference_genome.fa -f -U inputdata.fa -S OutputData.sam --no-hd --no-sq --no-unal -k 5 2> 'bowtie2_summary/inputdata.txt'
$\endgroup$
0

Your Answer

By clicking “Post Your Answer”, you agree to our terms of service, privacy policy and cookie policy

Not the answer you're looking for? Browse other questions tagged or ask your own question.