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## Bug Report
### Affected tool(s)
_Tool name(s), special parameters?_
RenameSampleInVcf
### Affected version(s)
- [ ] Latest public release version [version?]
- [ ] Latest development/maste…
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Per @sr320 - please identify possible samples for cod methylation sequencing.
kubu4 updated
4 months ago
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Hi Felix,
it's using bismark to handle the non-directional data, but I don't know how to judge CT/CTOT/CTOB/OB.
Logically, I think :
CT read1 with XR:Z:CT XG:Z:CT and rea…
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Hi Tobias,
Could you kindly help me with the following 2 questions?
1. The slam-seq library was prepared with Lexogen kits and should used single-end sequencing. But the sequencing center returned…
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I tried to run Bismark for Bisulfite sequencing data, the command was "bismark -p 4 --path_to_bowtie /bin/bowtie2-2.2.5 --bowtie2 /REFERENCES/human38/ -1 sample1_F.fq.gz -2 sample1_R.fq.gz, but after…
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I am working with whole-genome bisulfite sequencing (WGBS) data, which comprises paired-end sequences with approximately 2 billion reads per sample (1 billion for the forward read and 1 billion for th…
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Hi,
looks interesting. Is there any reason it could not handle nanopore data, eg output from modbam2bed ?
https://github.com/epi2me-labs/modbam2bed
We typically convert the output into bedg / b…
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Hi Felix,
I am trying to analyse RRBS data which were produced using the Diagenode Premium RRBS Sequencing Kit. The produced RRBS paired-end libraries were run in an Illumina Next-Seq 500 sequencer…
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I am trying to map paired-end reads from an amplicon sequencing using Bismark. The command line is
bismark --un --ambiguous --maxins 1000 --non_directional --score_min L,-0.6,-1 bismark-genome…
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Dear Felix,
I have methylation data from HBV cccDNA samples.
The experiment is like a target bisulfite sequencing but using different couples of primers to amplify several regions.
I'm studying h…