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BIMSBbioinfo / pigx_bsseq

bisulfite sequencing pipeline from fastq to methylation reports
https://bioinformatics.mdc-berlin.de/pigx/
GNU General Public License v3.0
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Error generating diffmeth reports #158

Closed srikanthkris closed 4 years ago

srikanthkris commented 4 years ago

Hi,

i am getting some error while generating diffmeth report.

it is due to non-standard chromosomal names in the bed file i think.

But not really sure which script file must be edited to tide over this.

The issue seems to be in ggbio/granges package. Attaching the log file below

Can you please help.

diffmeth-report.0vs1.log

alexg9010 commented 4 years ago

Hi @srikanthkris ,

Probably your error is due to this line: https://github.com/BIMSBbioinfo/pigx_bsseq/blob/master/report_templates/diffmeth.Rmd.in#L353 . It seems that some of your reads mapped to non-standard chromosomes.

When creating the ideoDMC plot we are subsetting to only these standard chromosomes, see here https://github.com/BIMSBbioinfo/pigx_bsseq/blob/master/scripts/ideoDMC.R#L119-L123 .

So depending on whether you trust the mapping to non-standard chroms you could try to remove https://github.com/BIMSBbioinfo/pigx_bsseq/blob/master/report_templates/diffmeth.Rmd.in#L353.

Or what I would suggest is to subset to all only standard chromosomes (https://github.com/BIMSBbioinfo/pigx_bsseq/blob/master/scripts/ideoDMC.R#L119-L123):

seqlevels(g.per, pruning.mode="coarse") = seqlevels(myIdeo)
[...]
seqlevels(g.po, pruning.mode="coarse") = seqlevels(myIdeo)

Hope this helps for now. I will be adding a fix for this as soon as possible, but if you installed the pipeline from github please feel free to fix it yourself and submit a pull request once it works.

Best, Alex

srikanthkris commented 4 years ago

Thanks alex for a super fast response. You are fantastic. That fixed it. I will try to make a pull request.