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Hello Felix,
I am a new user of Bismark. I am trying to map reads from targeted bisulfite sequencing (a set of 5 amplicons from human genome). After mapping, I get ~95% of mapped reads. In the repo…
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I used the following commands to run bismark:
/PUBLIC/software/RNA/bismark/bismark_v0.12.5/bismark -u 50000 -q --bowtie2 -p 4 --prefix map --path_to_bowtie /PUBLIC/software/RNA/bowtie2-2.2.5 -o map_t…
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I set a run last night and got the following errors marking duplicates in BAM files:
```
> grep -inr Exception runs/MARK-DUPS/*err
runs/MARK-DUPS/SS.11.10.err:20:Exception in thread "main" htsjdk…
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I'm getting an error when running the pipeline with the `--rrbs` switch; run starts trimming etc without `--rrbs`...
```
$ nextflow run $NF/bismark.nf -profile base --reads '*_R{1,2}_001.fastq' …
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Hi, I failed to run getMatrices.sh and got the error message: "Error using symengine
Unable to convert expression into double array." I didn't see symengine installed in the informMEdeps folder. Coul…
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I've noticed with a whole-genome bisulfite sequencing dataset (2x100bp, aligned using bwa-meth), that there's a huge difference between the samblaster discordant read extraction and the samtools read …
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Just wondering if CNVnator can be used on WGBS data, like the [readDepth](https://github.com/chrisamiller/readDepth) package.
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Hi Dr. Weilong,
Where I can find the definition to the reads which are not fully converted by bisulfite treatment?
I notice it before, however, I can not find it again when I need it.
Than…
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Hi, our lab have done WGBS on a kind of monkey. But the conversion rate of 3 sample is relatively low (only about 90%, the others are over 99%). Well 90% and 99% is from observation of fastqc report b…
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I’m eyeballing the methylation calls from methyldackel (Version: 0.3.0 (using HTSlib version 1.2.1) ) on my bam file ([bisulfite_test_bwameth.bam.zip](https://github.com/dpryan79/MethylDackel/files/11…