How to export summary data from Bowtie2 for MultiQC to read?

Question

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?

Stephan · Answer

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'

How to export summary data from Bowtie2 for MultiQC to read?

One Answer

Add your own answers!

Ask a Question