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Hi Felix,
First, thank you very much for your prompt reply to my previous question on Bismark. It helped to clear up things.
There is a polyA option in trim_galore that allows to trim off polyA …
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@FelixKrueger
I am using `bismark_methylation_extractor` for the first time. Would you please give me a guideline how to proceed.
1. I did a paired-end reads, a significant portion of each lane …
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The files
```
Sealice_F1_S20_L001_R1_001.fastq.gz
Sealice_F1_S20_L001_R2_001.fastq.gz
Sealice_F1_S20_L002_R1_001.fastq.gz
Sealice_F1_S20_L002_R2_001.fastq.gz
Sealice_F2_S22_L001_R1_001.fastq.gz
…
sr320 updated
4 years ago
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Trimmed
Bismark
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bismark_genome_preparation doesn't work for me because the container doesn't contain bowtie2-build -- did you test this @michalstolarczyk ?
```
bismark_genome_preparation --bowtie2 /home/nsheff/sa…
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Hi Ni Peng,
I am impressed by your deepsignal tools.
Our focus is on DNA methylation in plants, which not only including CG methylation, but also CHH and CHG. What's more, there are little data in …
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Dear Yupeng,
I am having trouble with running DMRfind for some of my datasets that were downloaded from NCBI (Arabidopsis bisulfite seq GSE67216). I used methylpy to generate the allC files and then…
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Hi Felix,
Hope you are well and safe in this global pandemic.
My issue is similar to this issue- https://github.com/FelixKrueger/Bismark/issues/184. But I am asking it here again as the post di…
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Hi All,
I was wondering if you can help me make a decision here. The sequencing core is asking me if I would like to add a balanced sample (PhiX) spike to my Bisulfite sequencing. I commented this…
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Hi Keegan,
dmrseq is incredible. Thanks so much for writing it! It's been wildly useful for my work. I am now embarking on yet another deconvolution idea from WGBS or other bisulfite-flavored seque…