-
Does the pipeline work for dna methylation data analysis in plants?
-
Hi,
I got an issue with bsrate function saying "bad line in MappedRead file". I had changed my bam file mapped by bismark using to-mr function, and when I used bsrate I got this problem. I wonder wh…
-
I'm running methylpy single-end-pipeline currently and it has been working very well!
Except that indexing is taking a very long time, and it only uses one core even though I set --num-procs 32. …
yvnkm updated
3 years ago
-
Hi Felix,
Thank you very mcuh for providing Bismark and help.
My question is why I got different mapping ratio results with similar parameters.
I ran two Bismark with same sample as follow:
comm…
-
Hi,
First of all I would like to congratulate for creating this tool. I'm working with low input bisulfite sequencing and I wanted to give it a try and compare to the current methodology I'm using.…
-
Hi Felix,
I am searching this document but I get out in the nirvana... ;D
http://www.epigenesys.eu/en/protocols/bio-informatics/483-quality-control-trimming-and-alignment-of-bisulfite-seq-data-prot…
-
Hi Felix,
I'm trying to align a publicly available dataset, and so far I'm getting quite abysmal alignment rates (around 8%). Doing a bit of research, I noticed that the bisulfite conversion kit th…
-
Nichole Rigby - 9:17 AM DEC 12
Not sure if this is a bug or not, but a single control probe shows up in the methylprep version of the manifest. Its one of the -99 ones. I'm guessing it should be in …
-
Dear Felix,
I got trimmed, synchronized but mixed orientations R1 and R2 files in an amplicon bisulfite sequencing experiment, and wanted to use pair-end alignment in bismark.
R1 and R2 have simi…
-
Hi @FelixKrueger !!
A while ago you recommended us [a trimming method](https://github.com/FelixKrueger/Bismark/issues/317#issuecomment-660146239) that worked wonders for our library prep. Some of o…