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I ran 123 workflows as part of a single submission in FireCloud which means, same WDL and identical inputs aside from the BAM and sample name. They all started around the same time.
3 failed wit…
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I am displaying WGBS data on the default mm10 genome that contains at some positions in the reference genome small letter bases (repeats etc.?) like ```act``` instead of ```ACT```. The default bisulfi…
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Hi Felix,
Do you think we can introduce a "function to remove reads with incomplete bisulfite conversion"
Regards,
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The following one-liner (which I Googled, so I cannot vouch that this is the best way to do things) revealed 245Mb of files that are unused in master:
for ff in `find src/test/resources -name "…
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Hi, I've been using Bismark for awhile to map some bisulfite PCR resequencing data, and overall performance has been good. Lately I've been attempting to improve the performance of my resequencing as…
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I'm seeking to identify potential methylation sites (CpG's) in my geoduck genome; although the CpG sites aren't definitive methylation sites, they have potential to be. I believe [CoGe](https://genom…
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Program: BISCUIT (BISulfite-seq CUI Toolkit)
Version: 0.2.0.20161222
```
$ biscuit align hg38.fa -t16 -p -c POETIC-11_R1.fastq POETIC-11_R2.fastq > output.bam
[M::bwa_idx_load_from_disk] read 0 …
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Update the following URL to point to the GitHub repository of
the package you wish to submit to _Bioconductor_
- Repository: https://github.com/shokoohi/DMCHMM
Confirm the following by editing …
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I do see a flash of a loading bar in 2.4 - but no authentication dialog like I get from 2.3.92
here are some tcpdump captures:
not working (2.4.5, 2.4.0)
```
08:54:58.559611 IP6 localhost.54271 …
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Once I have ran the analysis in CoGe and can view the methylation data, how can I export sequences in regions of interest in a usable format for blasting? To be specific, I can see how to look at sequ…