From c2d1aa3f41f6177e4ed1ed8c3909bb358ead15e4 Mon Sep 17 00:00:00 2001 From: atpoint Date: Fri, 4 Mar 2022 15:41:04 +0100 Subject: [PATCH] add some docs --- README.md | 7 ++++--- 1 file changed, 4 insertions(+), 3 deletions(-) diff --git a/README.md b/README.md index 8bf5876..fce65d4 100644 --- a/README.md +++ b/README.md @@ -8,7 +8,7 @@ calculating Fractions Of Reads Per Peaks (FRiPs).
-![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/) @@ -38,7 +38,7 @@ 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 @@ -46,7 +46,8 @@ NXF_VER=21.04.3 \ ## 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