bamCoverage not returning any results

usegalaxy.org support
1

Hello! I am having trouble getting any data using the bamCoverage tool on my mapped reads in BAM format. It shouldn’t be an issue with my files or the options I set in bamCoverage, because these exact files and options worked last week when I ran it, and now it is returning with 0 data. I tried restarting my browser, changing my browser, and running the tool in a different history, but none of these methods helped. Is there an issue with this tool or the server? I did notice there was an update in the server some time during this week and last week.

Here’s a copy of my history if that’s helpful: Galaxy

Thank you!!

1 Like
2

Hi @Wei,

I tested bedCoverage on the BAM file (dataset 8 in the shared history), and the job produced non-empty file, indicating that the software is functional, and the input file has no issue. I suspect the issue is caused by non-default (conflicting?) settings. Maybe start with the default settings and change parameters one by one, until you get an empty file.

Hope that helps.

Kind regards,
Igor