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### Instructions
- Use a **concise** yet **descriptive** title;
- Determine whether your issue is a **bug report**, a **feature request**, or a **documentation request**;
- Choose the correspondi…
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- [x] mRNAseq DESeq2
- [ ] mRNAseq sleuth
- [ ] noncoding RNAseq
- [ ] WGBS
- [ ] ATAC-seq
- [ ] ChIP-seq
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What's are everyone's / anyone's thoughts about making it case-insensitive? Example: right now, defining a `pipeline_args` section of a project config with `WGBS` and `RRBS` as section keys for opt/ar…
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Hello Dr. Heath,
I ran gemBS map and call in one sample (WGBS) and everything went well. Then, I added two other samples to my metadata.csv, deleted the .gemBS folder and reran gemBS prepare and inde…
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Hello,
Is adapter trimming required or recommended for WGBS analysis using gemBS?
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HI, hmyh2012. I am interested in WGBS, but i don't know how to analysis WGBS . Could you share your pipeline for us, thank you!
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This part of the pipeline always fails, for all samples. After a few different runs with different data sets, this always happens. However, the stats files actually _are_ generated, but I'm not sure w…
kubu4 updated
2 years ago
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Hi,
What is the recommended workflow for generating the required BAM files?
Also, what is the recommended tools for clustering wgbs samples? ie, samples from different tissues and then unbiased clust…
gevro updated
7 months ago
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Hi,
Does structural variant calling suggested [here](https://huishenlab.github.io/biscuit/docs/structural_variants.html) also work for targeted methylseq data?
Also, do you know of any tool/pipe…
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The code is as follows:
bismark --bowtie2 -p 10 --genome .. /st_8_bow2_idx/ --basename Stem_WGBS_rep1 -o 2.align/ -1 .. /1.cleandata/Stem_WGBS_rep1_R1_clean.fq.gz -2 .. /1.cleandata/Stem_WGBS_rep1_R2…
yhj-j updated
8 months ago