MareikeJaniak
commented
2 months ago Hi Shaloo, Yes, good idea. We can talk about it more, but here would be some of my suggestions, based on questions we get frequently.
- New users sometimes don't realize that they need to also run
bash genpipes_command.shafter running the genpipes command, so they don't understand why no jobs have been submitted. - Many questions and issues are due to the readset and/or design file not being formatted correctly. A reminder to double check these things with a link to the relevant page would be useful.
- Users often see very low mapping rates (close to 0%), which is usually resolved by flipping the R1 and R2 reads, so R2=FASTQ1 and R1=FASTQ2.
shaloo
List top 3-5 issues faced by new users when deploying, using genpipes 5.0. Suggest solutions/workarounds
Update existing troubleshooting guide with a new section on GenPipes 5.0 here: https://genpipes.readthedocs.io/en/genpipes-v4.6.0/development/troubleshooting_guide.html
cc: @MareikeJaniak @pphector
Can you pls share top 3 issues faced and recommended way out / solutions for new users GenPipes 5.0? If you'd like to have a quick huddle/call lmk. Preferably Tue/Wed 9-10am or 11:30am-12pm Montreal, Canada time.