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We should change the way how the sample sheet is parsed /accessed (here https://github.com/BIMSBbioinfo/pigx_bsseq/blob/master/pigx-bsseq.in#L142-L184) to the way how the rna-seq did (here https://gi…
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Hi,
I'm currently using DSS to analyze 18 WGBS samples for differential methylated sites. I'm would like to run multifactor contrast to test for interaction effects among my treatments. However, af…
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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…
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Hi Jared and Thanks for this tools.
I am trying to clone and run it but it seems like I am missing something or that something is missing in the repo.
There is no make or bash file and simply r…
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`combineList()` is strict in its requirement of not allowing for overlapping `sampleNames` across the objects. However, this is sometimes perhaps too strict, e.g., combining CHG and CHH _BSseq_ object…
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**1. Suppl Figure 1**
- [x] A. FACS plots of PND8 and PND15 spermatogonia isolation (Irina)
- [x] B. Immunocytochemistry (ICC) of sorted vs unsorted spermatogonia population (Irina)
- [x] C. …
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Hi Christa,
Thank you for developing CelFiE. I am trying to run CelFiE on 2 samples (adult normal lung tissues-WGBS). After getting the coverage file from Bismark, I ran your prepare_bismark.sh scr…
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Hi,
Thanks for the methylation analysis pipeline.
I was testing a human WGBS data with msPIPE, and I used UCSC hg38 for reference. When running with run_MethylSeekR.pl, I got the following error…
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Hi Dinh,
I'm running your tool to extract methylation haplotypes from bam files, and I'm currently comparing the reads displayed in IGV with the methylation haplotypes generated from your tool. I'm…
caalo updated
6 years ago
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Dear author:
Thank you for develop such a useful tools for WGBS. I have run a methylpy pipeline for one month at least. How ever, my output sam files are still renewed. My log is displayed below. C…