Felix Krueger

Dear Yingchuo Hu, I believe you are running into an issue that has come up before, and I have tried to summarise it here: https://felixkrueger.github.io/Bismark/faq/context_change/ Could you take a look...

I am not quite sure I understand the question "so why would deletion happen". Generally, the mapping is carried out first, and then the methylation call is performed afterwards. ```...

Hmm, could you raise this issue over that bioconda?

Assuming the human genome, and easy to work numbers, a single run of Bismark requires ~3 cores (at 100%) and ~14GB of RAM for a standard directional run, and 5...

That still sounds like memory issues, what did you change? Can you google `(ERR): bowtie2-align died with signal 9 (KILL)`?

Regarding 1: in the first instance I would try to see if Bismark runs fine without `--multicore 12` with a sample command: ``` bismark --genome path/genome_dir --output_dir path/alignment -1 filename_R1.fq.gz...

In the default mode, Bismark will require 3 cores at 100%, and ~ 10-15GB of RAM for default. Any factor of `--multiple` will multiply these requirements (see `--help` for more...

Not exactly sure what the memory requirements are for the T2T genome, but I doubt it will be lower than GRCh38. the option `--parallel/--multiple` are equivalent. The most important thing...

There are at least a dozen different types of BS-seq, it is important to know specific details (e.g. Accel Swift, PBAT, scNMT, WGBS, RRBS...)

Simplifying the name has no effect (other than a different file name...): ``` ln: GSM7506206.fastq.gz: File exists ln: GSM7506206.fastq.gz: File exists ln: GSM7506206.fastq.gz: File exists ln: GSM7506206.fastq.gz: File exists ln:...