NextGenMap for bisulfite data and methylation calling about nextgenmap

[fritzsedlazeck]

Dear Chema,
thanks for reaching out. Its been a while since I worked on the bisulfite mapping code. Could you also try the sam output as I am not sure if the bam output was tested well for this mode.

Last time I used it was for this: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4413256/
where we used a script from bismark in the end to compute the mehtylion profile based on the mapped reads.

Hope that helps
Thanks
Fritz

[ChemaMD]

Dear Fritz,

Thanks for your reply! Ok, I will re-run it keeping the SAM output. I have a question regarding these two options:

-d/--pe-delimiter <char>      Character used in suffix that identifies mate 1
                           and 2. E.g. /1 and /2. This suffixes will be
                           removed to ensure proper SAM output
                           (default: /)
--keep-tags                   Copy BAM/SAM tags present in input file to
                           output file (default: off)

Should I include --keep-tags? and what about the PE suffixes?

Cheers,

Chema

[fritzsedlazeck]

Its been a while, but I think they are only if you use a bam file as input.
I wouldn't
Thanks
Fritz