MOABS: mcall - Githubissues

MultiQC / MultiQC

Aggregate results from bioinformatics analyses across many samples into a single report.

http://multiqc.info

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MOABS: mcall #847

Open sklages opened 5 years ago

sklages commented 5 years ago

Tool Details

Name of tool: mcall from MOABS package
Tool homepage: https://github.com/sunnyisgalaxy/moabs
Tool description: DNA Methylation Caller
Data suitable for MultiQC plot(s): per chromosome methylation rates? Strand specific stats?
Most interesting data for General Stats table: alignment stats, methylation stats

Tool output:

Log filename pattern: *.bam.G.bed *.bam_stat.txt, may be altered by user

sklages commented 5 years ago

mcall.out.txt

ewels commented 5 years ago

Thanks @sklages - looks like an interesting tool! Is the attached example the standard out? What's in *.bam_stat.txt?

sklages commented 5 years ago

This is the standard mcall output, just the file I attached. I gave it a bad name (mcall.out.txt) .. I rename both the bed and the bam_stat file in my scripts/pipelines, because mcall always gives the same name for the files, no matter if I call CpG, CpA, CpT or CpC ...

So maybe you should not only rely on the filename, but also on the content (at least for files with txt extension and a filesize less than e.g. 1M)?

sklages commented 5 years ago

stdout looks like this (could be captured to file as well): mcall.stdout.txt

demis001 commented 4 years ago

Is this implimented or a task on progress? I used MOABS to process the data.

ewels commented 4 years ago

It's in the queue for new modules - no-one has said that they are working on it yet, so PRs to add it are welcome (see docs). I will hopefully get to it at some point, but there is a lot of other work ahead of this in the queue I'm afraid, so it may take me a long time.