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### Is there an existing module for this?
- [X] I have searched for the existing module
### Is there an open PR for this?
- [X] I have searched for existing PRs
### Is there an open issue …
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## Bug Report
### Affected tool(s)
picard UmiAwareMarkDuplicatesWithMateCigar
### Affected version(s)
- [ ] Latest public release version [2.21.6]
### Description
When multiple fragments …
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How do I activate define the GPU for read mapping?
I did go though the working example and used nvidia-smi to monitor any potential activity on the GPU: I could not find any.
For the gem3-mapper I…
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A message from Vince on [slack](https://community-bioc.slack.com/archives/CM2CUGBGB/p1677310530239179)
> query on ch 12 that addresses CITEseq with ADT counts in altExp vs SingleCellMultiModal that…
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Hi,
First thanks to build this package it is very interesting tool.
So I'm trying to integrate your package in my ATACseq pipeline.
But I have some issue. In fact, when I trying to build the "g…
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New issue so we can keep a track of running of scripts.
I'm currently test-running the annotation pipeline on the cluster, without PhaseMatch2. I've edited the size classes based on the density plo…
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### Aims/objectives.
We currently have BID-seq, eTAM-seq, and GLORI, amounting to a total of 65 dataset. We need to add more data from the public domain, esp. if we aim for a publication. We cannot…
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@jrobinso @mschatz @marcus1487
Split from #1133. Related to #1153.
This issue splits from #1133, which provides nice support for visualizing 5mC methylation (C+m in MM tag), to support other ma…
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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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**Describe the bug**
See subject.
**To Reproduce**
Steps to reproduce the behavior (steps 1-8 for data preparation):
1. wget --directory-prefix=data https://ftp.ncbi.nlm.nih.gov/geo/samples/GSM5…