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Hi fellow Datathoneers,
Thank you very much for taking part in the second GCC Datathon. We hope you had a good experience. In order to get an overview on current and potential future Datathon activit…
cschu updated
8 years ago
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I use STAR happily and effectively for genome alignment workflows (e.g. CHiP/ATAC-Seq).
Some approaches to downstream analysis required comparing read counts in genomic "bins" (e.g. one bin every t…
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## **Description of bug**
I've installed caper and the pipeline in a conda environment and I'm trying to run it with example config/data from the repo thusly:
```
$ git clone https://github.com/e…
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Hello,
How can I run this pipeline for paired end reads
Thank you
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Hi,
first of all, thank you for providing a wonderful tool. I ran the ATAC-seq analysis using the pipeline on data as shown below
1. control -> no replicate
2. sample -> 2 biological replicate.
…
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### Description of the bug
Hello,
I am trying to run GSEA but I get an error when trying to process the GMT file I obtained from MSigDB.
Previously, I have executed the pipeline without the G…
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@sitag @dbujold
The _total_reads_ count is done by parsing the flagstat file and corresponds to the "in total" value but if we don't substract the "secondary" value we can end up with more reads t…
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## Description
A quick description of the repository on GitHub would be nice for metadata reasons (it would also look nicer on the lab website this way).
![image](https://github.com/user-attachm…
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A "as simple as possible" init script usable for each DEEP pipeline that identifies itself (WGBS, ChIP-seq etc.) and loads - if necessary - required reference data/configurations from the reference re…
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I am running nextflow DSL2 multiruns and first testing it on a small no of runs 2 to see if it is working on a few runs before doing a much larger no of runs. I have a loom file that I created from pr…