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Hi,
I am working with WGBS data from a triploid organism and would like to perform SNV calling using CGmapTools. The BayesWC strategy is based on the assumption of diploid genome. Would it be possibl…
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Dear Prof. Li
Very good software！
I have a question, because the data we used to analyze WGBS is relatively large, and there are many samples, the sequence alignment process takes more time, so we …
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Hi, I would like to use your package for the analysis of RRBS data. First of all, do you think it is appropiate to use Mathylinheritance with RRBS data or should it be only fro WGBS? Can or should I m…
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A "as simple as possible" init script usable for each DEEP pipeline that identifies itself (WGBS, ChIP-seq etc.) and loads - if necessary - required reference data/configurations from the reference re…
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I'm aligning PE WGBS data using a Bismark wrapper for the bowtie2. Recently, I switched from bowtie2 2.4.2 to the latest 2.5.2 and faced a memory issue.
(P.S: bowtie2 2.4.5 works consumes const mem…
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I am new to bioinformatics and I am trying to analyze WGBS data using BSseeker2. I am using Python 2.7.13 with Pysam 0.9.1.2. bs_seeker2-align.py terminates after running for 9 minutes indicating an e…
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Hi, I was wondering if you or someone has used your algorithm and reference atlas to deconvolute whole genome bisulfite methylation sequence data (WGBS)? I tried using it for some samples but, it pred…
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I have genotype array, WGS, and WGBS data for my samples. I am using this information to detect sample swaps. I find that Biscut genotype calls are highly concordant with WGS genotype calls except for…
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Calling DMR (DMLtest with smoothing) from a 2 vs. 2 WGBS data costs about 20 hrs, no matter the workers= 200 or workers=100 in MulticoreParam. (The total cores in the machine are 256.)
The real CPU u…
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Hello,
I am trying to run mcall module but segfaulting. I've tried to google/solve it myself, but I haven't had any success.
I am running a target position specific bisulfite sequencing (not WG…