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I am running CGMAPTOOLS to get ASM calls from WGBS data on my sample. I ran the CGMAP step to convert to the ATCG format, performed SNV calling (bayes mode) and eventually submitted the job for ASM …
nmfad updated
8 months ago
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I'm trying to run the pipeline test via the Singularity image on our university's computing cluster, which doesn't have internet access when executing jobs.
I've downloaded all the of the input fil…
kubu4 updated
2 years ago
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After marking dupes, the following
biscuit pileup -q 16 -r hg19.fa -i WGBS_$SAMPLE.mkdups.hg19.bam -o WGBS_$SAMPLE.mkdups.hg19.vcf
fails on a number of samples (4/6, not all though). Is there a st…
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Hi!
I am trying to BSMAP using following command line:
"BSMAPz/bsmapz -a /media/waqas/30004AFD3CB35412/All_Data/WGBS-Seq/epiRIL-368/Raw/epiRIL-368_QC_Reads_WGBS/Epiril368_4_C_R1_L001_R1_val_1.fq.g…
CS791 updated
3 years ago
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**A reproducible template workflow for single-cell DNA methylation data**
DNA methylation is a heritable epigenetic mark that shows a strong correlation with transcriptional activity, and may be de…
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Hello,
After I installed the package, I found I can't upload the data. My error massage show below. Can you give me some advises. Thank you very much!
> fs_wgbs
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Ran the following command to test installation:
`NXF_VER=20.07.1 /home/shared/nextflow run epidiverse/wgbs -profile test,docker`
The test fails in the following fashion:
```
[7f/7c58ce] proc…
kubu4 updated
2 years ago
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samtools version 1.9
trim_galore version 0.6.4_dev (dependency fastqc and cudadapt v. 2.8)
biscuit version 0.3.8.20180515
bamtools version 2.5.1
picard version 2.18.15-snapshot
wgbs_tools = gith…
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Hi yupeng,
I've obtained a batch of processed WGBS data from GEO database, which was generated using the 'methylpy allc-to-bigwig --bin-size 10' command, resulting in 10 bp bin format files (e.g., …
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Hi,
In your paper you have mentioned that "dmrseq is generally applicable to WGBS data". My impression is that methods that work for WGBS also work for RRBS data. Have you tried dmrseq for RRBS data?…