Bismark
Bismark copied to clipboard
FelixKrueger
A tool to map bisulfite converted sequence reads and determine cytosine methylation states
I am executing the bismark on paired end data using the command: bismark --multicore 12 path/genome_dir --output_dir path/alignment -1
Hi, We do 10x deeper scNMTseq than that are used in typical scNMTseq experiments. However, during the coverage2cytosine portion of the pipeline, for each cell, I need at least 400GB...
Hi FelixKrueger, I am little confused about the number of detected Cytosine in `CX_report.txt` and `bismark.cov.gz.` With the option `--CX`, the coverage file (`bismark.cov.gz.`) is extended to cytosines in any...
Hello! I have used this program to extract the DNA methylation levels from data and have bam outputs. I am trying to analyze where methylation is occurring on the genome,...
Hi, I am currently using Bismark for my DNA methylation analysis and have a question regarding the post-alignment filtering process. Specifically, I'm using the --local parameter for alignment, which I...
The code is as follows: bismark --bowtie2 -p 10 --genome .. /st_8_bow2_idx/ --basename Stem_WGBS_rep1 -o 2.align/ -1 .. /1.cleandata/Stem_WGBS_rep1_R1_clean.fq.gz -2 .. /1.cleandata/Stem_WGBS_rep1_R2_clean.fq.gz 1>2.align/Stem_WGBS_rep1.log 2>&1 How to solve the error as...
Hi, I am running methylation_extractor and the process gets stuck. I have run this successfully in the past. the output error last lines are: ``` Processed lines: 554500000 Finished processing...
Hi, I decided to re-align data (I aligned it ~1-2 years ago) and faced with memory issues. Before memory usage was constant, and now it is linear with time. I'm...
Hi, I'm working with short-read, enzymatic converted human genome reads produced by nanopore. The expected read-lenght is about 150-200bp; + additional Illumina adaptors + nanopore adaptors; so i trimmed the...
Metadata
Owner
Metadata
A tool to map bisulfite converted sequence reads and determine cytosine methylation states