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https://github.com/jkobject/slamdunk
A Terra and paired End Enabled Slamdunk: Streamlining SLAM-seq analysis with ultra-high sensitivity
https://github.com/jkobject/slamdunk
Last synced: 3 months ago
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A Terra and paired End Enabled Slamdunk: Streamlining SLAM-seq analysis with ultra-high sensitivity
- Host: GitHub
- URL: https://github.com/jkobject/slamdunk
- Owner: jkobject
- License: agpl-3.0
- Fork: true (t-neumann/slamdunk)
- Created: 2019-12-17T21:18:59.000Z (about 5 years ago)
- Default Branch: master
- Last Pushed: 2022-05-18T18:39:17.000Z (over 2 years ago)
- Last Synced: 2024-08-03T01:11:54.333Z (6 months ago)
- Language: Python
- Homepage:
- Size: 39.4 MB
- Stars: 0
- Watchers: 1
- Forks: 2
- Open Issues: 0
-
Metadata Files:
- Readme: README.md
- License: LICENSE
Awesome Lists containing this project
- AwesomeGenomics - JK/slamdunk
README
## jkobject/slamdunk
A spike-in enabled and paired-end sequencing compliant version of slamdunk.
## Installation
`pip install git+https://github.com/jkobject/slamdunk`
! Make sure that you have installed [ngm](https://github.com/Cibiv/NextGenMap/wiki) too.
! if you have paired end reads or use hg38, please read the remarks bellow.
## Remark
You should think about trimming ends from your reads before running slamdunk.
See some additional tips and advices about running slamdunk in our issue report here:
- [Signal at alternate contigs lost #107](https://github.com/t-neumann/slamdunk/issues/107)
- [Multimapping influences output at read length of 152bp #106](https://github.com/t-neumann/slamdunk/issues/106)
- [Multimapping is not default and bed file isn't used #105](https://github.com/t-neumann/slamdunk/issues/105)
### t-neuman Slamdunk documentation
http://t-neumann.github.io/slamdunk
### citation:
please cite both the initial paper from t-neuman: [Quantification of experimentally induced nucleotide conversions in high-throughput sequencing datasets](https://bmcbioinformatics.biomedcentral.com/articles/10.1186/s12859-019-2849-7) and our own paper on the topic [A distinct core regulatory module enforces oncogene expression in KMT2A-rearranged leukemia](https://www.biorxiv.org/content/10.1101/2021.08.03.454902v1.abstract)
Updated by:
- Jeremie Kalfon @jkobject
- Monika Perez