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