wgbs_tools
wgbs_tools copied to clipboard
nloyfer
tools for working with Bisulfite Sequencing data while preserving reads intrinsic dependencies
Hi, wgbstools is a good tool for DNA methylation data analysis, but I wonder if it could generate single base CG and CH methylation allc files which are compatiable to...
Hallo i am using wgbstools to visualize my Nanopore Data. So everything worked but i have a few questions regarding the Output. I segmented the Bam file and vis it...
Hi guys, Amazing tools! Are there any plans to include functionality in `bam2pat` to handle nanopre modbams with MM and ML tags? If not, what could be a good way...
Compiling stdin2beta... SUCCESS Compiling mask_pat... SUCCESS Compiling pat_sampler... SUCCESS Compiling patter... SUCCESS Compiling bp_patter... SUCCESS Compiling snp_patter... SUCCESS Compiling match_maker... SUCCESS Compiling segmentor... SUCCESS Compiling cview... FAIL Failed compilation. Command:...
Code: ./wgbstools init_genome -h Output error: Invalid command: init_genome did you mean init_genome?
Dear All, Thanks for your efforts. Steps follow. \# Clone git clone https://github.com/nloyfer/wgbs_tools.git cd wgbs_tools \# compile python setup.py module load anaconda3/5.1.0 gcc/8.5.0 samtools/1.16.1 htslib/1.19 export PATH=$PATH:$PWD cd wgbstools init_genome...
Hello, I tried to split the beta (hg19) of the cell_WGBS in the paper : $ wgbstools segment --betas *beta --min_cpg 3 --max_bp 2000 -o blocks.small.bed The following error occurred：...
I got an error as "FileNotFoundError: [Errno 2] No such file or directory: '/home/qyjing/softwares/wgbs_tools/references/default'", even though I have set the parameter "--genome hg19 ". Before I run bam2pat, i have...
Hi, thanks for developing this useful tool! However, I had some problems when I wanted to convert my WGBS data to 850K array data, I trying to use beta_to_450k to...
Hi, What is the recommended workflow for generating the required BAM files? Also, what is the recommended tools for clustering wgbs samples? ie, samples from different tissues and then unbiased...
