Join GitHub today
GitHub is home to over 28 million developers working together to host and review code, manage projects, and build software together.Sign up
iRep_filter.py overwrites coverage table with relative abundance table when run twice #24
I noticed, that when iRep_filter.py is run twice (e.g., first collating genomes, then samples), the coverage information gets lost.
Here is a minimal example:
when i run
Notice how these sections are suddenly identical
It’s not shown in this example, but I have observed, that when the coverage values are replaced with the wrong "relative abundance" values, they seem to be used for coverage filtering, which can result in loosing valid iRep values.
As a workaround, removing the
This is the command I use the process the files before merging them: