Hello. I am using bowtie2 for my ChIP-seq analysis but not seeing the “tool standard error” for most of my files, though I can see that the job is successfully performed. It is coming up as “empty”. Consequently, I am not being able to see the alignment rate, reads aligned etc. I am new to bioinformatics tools and relying on Galaxy for all my sequencing analysis. Could you please help with this? I will be grateful.
Thank you.
Hi @TIRTHANKAR_BANDYOPAD,
which version of the tool are you using , and on which Galaxy server are you working?
With toolshed.g2.bx.psu.edu/repos/devteam/bowtie2/bowtie2/2.5.0+galaxy0 on usegalaxy.eu, the stderr is not empty at least.
Also, have you seen the option “Save the bowtie2 mapping statistics to the history”? This will redirect the mapping stats you are looking for from stderr to an extra dataset in your history.
Cheers,
Wolfgang
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