https://github.com/y9c/m6a-camseq
🧪 m6A-CAM-seq
https://github.com/y9c/m6a-camseq
bioinformatics epigenetics rna
Last synced: about 1 month ago
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🧪 m6A-CAM-seq
- Host: GitHub
- URL: https://github.com/y9c/m6a-camseq
- Owner: y9c
- License: gpl-3.0
- Created: 2024-06-02T20:29:24.000Z (about 1 year ago)
- Default Branch: main
- Last Pushed: 2025-02-28T18:29:18.000Z (3 months ago)
- Last Synced: 2025-04-09T06:35:03.833Z (2 months ago)
- Topics: bioinformatics, epigenetics, rna
- Language: Python
- Homepage: https://camseq.chuan.science
- Size: 6.3 MB
- Stars: 5
- Watchers: 1
- Forks: 0
- Open Issues: 0
-
Metadata Files:
- Readme: README.md
- License: LICENSE
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README
# m6A-CAMseq
## Qucik start
- Prepare configuration file
_minimum configuration example:_
```yaml
reference:
genes:
- ./ref/spike-in.fa
- ./ref/Arabidopsis_thaliana.rRNA.fa
genome:
- /data/reference/genome/Arabidopsis_thaliana/TAIR10.fa
# TODO: automatically generate index (?)
genome_index: /data/reference/genome/Arabidopsis_thaliana/hisat2_tx_3n/TAIR10.release57
samples:
test1:
- R1: ../test/test_R1.fq.gz
R2: ../test/test_R2.fq.gz
```
_advanced configuration:_
```yaml
# set library preparation method
# can be "STRANDED", "ECLIP10", etc, refer to the cutseq documentation for more information
libtype: STRANDED
# by default, the pipeline will use the strandness information from the library
# if the strandness is not available, set the strandness to `false`
strandness: true
# by default, the pipeline will force remove the PCR duplicates based on the UMI
# if UMI is not available, you can toggle the markdup to `false` to skip the PCR duplicate removal
markdup: true
```
- Install apptainer and run
```bash
apptainer run -B /data docker://y9ch/camseq -c data.yaml -j 48
```
## Customization
System Requirements
This package has been tested on Linux operating systems. It requires the following software dependencies:
- [Python](https://www.python.org/downloads/) 3.7 or higher
- [Snakemake](https://snakemake.readthedocs.io/en/stable/getting_started/installation.html) 8.0.0 or higher
- [hisat2-3n](https://github.com/DaehwanKimLab/hisat2/tree/hisat-3n)
- cutseq
## Documentation
The documentation is available at [https://y9c.github.io/m6A-CAMseq/](https://y9c.github.io/m6A-CAMseq/)
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Copyright © 2023-present
Chang Y