wgbs_tools
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nloyfer
tools for working with Bisulfite Sequencing data while preserving reads intrinsic dependencies
Hi there. Thanks for this great suite of tools. I wanted to create larger, more contiguous blocks solely focused on the patterin brain cells. For this, I subset your .beta...
It seems bam2pat for nanopore data has some problem in recognising [ "eXtended CIGAR", or CIGARX string](https://timd.one/blog/genomics/cigar.php). ``` 8,229,233,213,224,53,229,57,235,252,255,255,115,249,247,185,231,247,57,139,181,235,251,74,126,165,34,254,255,170,186,193,255,255,254,241,235,237,255,255,254,238,225,14,254,238,253,255,66,254,254,247 RG:Z:c969ee83 mc:f:99.5874 mg:f:99.6108 NM:i:72 [ patter ] [ patter ] Unknown...
I am attempting to run mix_pat to make different proportions of test data for wgbstools and UXM, but keep hitting the same issue. When I run the command: `wgbstools mix_pat...
Hi! Thank you for developing these great tools! I was wondering what would be the recommended way to convert pat files from one genome to another? As far as I...
Hi, I believe the bed files emitted from this tool use a non-standard start and end position. The bed files from wgbs_tools appear to be 1-based for the start when...
Hi, I found a large dataset listed on the EpiRR project which contains '.fractional.bw' bigwig files. I'd like to display these samples side-by-side with other samples for which I've already...
Hi, is there a way to convert 450k data to beta or pat format? I am interested in comparing the data from the Nature atlas paper and the data from...
Congrats on the paper! These are lovely tools, but the research use only restriction / noncommercial limit for .pat/.beta will likely limit adoption. Would y'all consider relicensing just that component...
Thank you for this nice software package! I was looking into the find_markers functionality, which allows to define specified comparisons between two groups of samples via the targets and background...
