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add some docs
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ATpoint committed Mar 4, 2022
1 parent 458cab4 commit c2d1aa3
Showing 1 changed file with 4 additions and 3 deletions.
7 changes: 4 additions & 3 deletions README.md
Original file line number Diff line number Diff line change
@@ -8,7 +8,7 @@ calculating Fractions Of Reads Per Peaks (FRiPs).

<br>

![CI](https://github.com/ATpoint/atac_chip_preprocess/actions/workflows/basic_test.yml/badge.svg)
![CI](https://github.com/ATpoint/atac_chip_preprocess/actions/workflows/CI.yml/badge.svg)
[![Nextflow](https://img.shields.io/badge/nextflow%20DSL2-%E2%89%A4%2021.04.3-23aa62.svg?labelColor=000000)](https://www.nextflow.io/)
[![run with conda](http://img.shields.io/badge/run%20with-conda-3EB049?labelColor=000000&logo=anaconda)](https://docs.conda.io/en/latest/)
[![run with docker](https://img.shields.io/badge/run%20with-docker-0db7ed?labelColor=000000&logo=docker)](https://www.docker.com/)
@@ -38,15 +38,16 @@ add additionally the `--atacseq` flag.
NXF_VER=21.04.3 \
nextflow run atpoint/atac_chip_preprocess -r 2.0 -profile singularity,slurm -with-trace -with-report report.html \
--idx path/to/idx/idxbasename \
--fastq "$(pwd)"'/*_{1,2}.fastq.gz' \
--fastq path/to/fastqfolder/*_{1,2}.fastq.gz' \
--align_threads 12 --sort_threads 2 --sort_mem '4G' --queue 'normal' \
-bg > report.log
```
## Pipeline
- trim reads with `cutadapt`, either the TruSeq adapter (default) or the Nextera adapter (default is using `--atacseq`)
- trim reads with `cutadapt`, either the TruSeq adapter (default) or
the Nextera adapter (default if using `--atacseq`)
- map trimmed reads with `bowtie2` and mark duplicates with `samblaster`
- remove unmapped reads, alignments with MAPQ < 20, mitochondrial alignments (for ATAC-seq), alignments to non-primary chromosomes,
non-primary and supplementary alignments, PCR duplicates

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