Commit 41fcff0b authored by Venkat Malladi's avatar Venkat Malladi
Browse files

Updated changes suggested by Spencer and fix pipeline error.

parent 5f54d2ec
Pipeline #3779 failed with stages
in 549 minutes and 2 seconds
# **CHIPseq Manual**
## Version 1.0.0
## January 2, 2019
## May 2, 2019
# BICF ChIP-seq Pipeline
......@@ -17,7 +17,7 @@ BICF ChIPseq is a bioinformatics best-practice analysis pipeline used for ChIP-s
The pipeline uses [Nextflow](https://www.nextflow.io), a bioinformatics workflow tool. It pre-processes raw data from FastQ inputs, aligns the reads and performs extensive quality-control on the results.
This pipeline is primarily used with a SLURM cluster on the [BioHPC Cluster](https://portal.biohpc.swmed.edu/content/). However, the pipeline should be able to run on any system that Nextflow supports.
This pipeline is primarily used with a SLURM cluster on the [BioHPC Cluster](https://portal.biohpc.swmed.edu/content/). However, the pipeline should be able to run on any system that supports Nextflow.
Additionally, the pipeline is designed to work with [Astrocyte Workflow System](https://astrocyte-test.biohpc.swmed.edu/static/docs/index.html) using a simple web interface.
......@@ -54,11 +54,11 @@ $ git clone git@git.biohpc.swmed.edu:BICF/Astrocyte/chipseq_analysis.git
+ This pipeline has been optimized for the correct partition
+ See [HERE](docs/CHIPseq.sh) for an example bash script
+ The parameters that must be specified are:
- --reads '/path/to/files/name.fastq.gz'
- --designFile '/path/to/file/design.txt',
- --reads '/path/to/files/name.fastq.gz'
- --designFile '/path/to/file/design.txt',
- --genome 'GRCm38', 'GRCh38', or 'GRCh37' (if you need to use another genome contact the [BICF](mailto:BICF@UTSouthwestern.edu))
- --pairedEnd 'true' or 'false' (where 'true' is PE and 'false' is SE; default 'false')
- --outDir (optional) path and folder name of the output data, example: /home2/s000000/Desktop/Chipseq_output
- --outDir (optional) path and folder name of the output data, example: /home2/s000000/Desktop/Chipseq_output (if not specficied will be under workflow/output/)
## Pipeline
+ There are 11 steps to the pipeline
......@@ -145,7 +145,7 @@ Please cite individual programs and versions used [HERE](docs/references.txt). P
+ macs/2.1.0-20151222 [website](http://liulab.dfci.harvard.edu/MACS/) [citation](docs/references.txt)
+ UCSC_userApps/v317 [website](https://genome.ucsc.edu/util.html) [citation](docs/references.txt)
+ R/3.4.1 [website](https://www.r-project.org/) [citation](docs/references.txt)
+ SPP/1.14
+ SPP/1.14
+ meme/4.11.1-gcc-openmpi [website](http://meme-suite.org/doc/install.html?man_type=web) [citation](docs/references.txt)
+ ChIPseeker [website](https://bioconductor.org/packages/release/bioc/html/ChIPseeker.html) [citation](docs/references.txt)
+ DiffBind [website](https://bioconductor.org/packages/release/bioc/html/DiffBind.html) [citation](docs/references.txt)
......@@ -154,6 +154,3 @@ Please cite individual programs and versions used [HERE](docs/references.txt). P
## Credits
This example worklow is derived from original scripts kindly contributed by the Bioinformatic Core Facility ([BICF](https://www.utsouthwestern.edu/labs/bioinformatics/)), in the [Department of Bioinformatics](https://www.utsouthwestern.edu/departments/bioinformatics/).
......@@ -2,4 +2,4 @@ sample_id experiment_id biosample factor treatment replicate control_id fastq_re
A1 A tissueA H3K27AC None 1 B1 A1.fastq.gz
A2 A tissueA H3K27AC None 2 B2 A2.fastq.gz
B1 B tissueB Input None 1 B1 B1.fastq.gz
B2 A tissueB Input None 2 B2 B2.fastq.gz
B2 B tissueB Input None 2 B2 B2.fastq.gz
......@@ -521,7 +521,8 @@ process motifSearch {
script:
"""
module load R/3.3.2-gccmkl
module load meme/4.11.1-gcc-openmpi
module load bedtools/2.26.0
python3 $baseDir/scripts/motif_search.py -d $designMotifSearch -g $fasta -p $topPeakCount
"""
}
......@@ -556,8 +557,7 @@ process diffPeaks {
"""
module load python/3.6.1-2-anaconda
module load meme/4.11.1-gcc-openmpi
module load bedtools/2.26.0
module load R/3.3.2-gccmkl
Rscript $baseDir/scripts/diff_peaks.R $designDiffPeaks
"""
}
......
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