methylseq
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nf-core
Methylation (Bisulfite-Sequencing) analysis pipeline using Bismark or bwa-meth + MethylDackel
Hi all, Does this pipeline handles spike ins (like the PhiX from illumina)? thank you in advance
Hi all, @FelixKrueger @ewels I tried to run the pipeline with some data, but I had no idea about how they have been produced. I know just that they are...
I noticed two hard-coded settings for bismark that are only for paired-end calls https://github.com/nf-core/methylseq/blob/62d30e1d06d194047a372be60e4755fd8d0e9281/main.nf#L511-L512 Should these be moved into parameters?
You may also want to look in to BitMapperBS, a new methylation calling tool, which seems very interesting given the Time and Sensitivity improvements over the other tools. Check the...
Version `2.6` of [nf-core/tools](https://github.com/nf-core/tools) has just been released with updates to the nf-core template. This automated pull-request attempts to apply the relevant updates to this pipeline. Please make sure to...
- [x] Merge [#242](https://github.com/nf-core/methylseq/pull/242) to get up to date with the template - [x] Try to resolve nf-core lint stuff, eg. updating modules - [ ] Finish multicore Bismark module...
### Description of the bug I have previously processed the GRCh38 genome with bwameth for a different pipeline that I'm trying to compare with the nf-core. So I provide the...
### Description of the bug Hi. I'm encountering an error with the methylsig pipeline when using bwameth aligner. The pipeline runs fine with Bismark, but my mapping is low (~40%)...
