Comments (3)
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
from nextgenmap.
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
from nextgenmap.
Its been a while, but I think they are only if you use a bam file as input.
I wouldn't
Thanks
Fritz
from nextgenmap.
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from nextgenmap.