Repository files navigation

Dependencies:

• trim_galore: version 0.6 or above (should be in path onbiohpc)
• multiqc: install multiqc using the following command:pip install --user multiqc
• STAR: version 2.7.0e or above (add to pathexport PATH=/programs/STAR:$PATH)
• RSeQC: version 2.61 (add to path using this guidelinebiohpc)

Usage:

nohup bash 3.4.sh "[-h arg] [-p arg] [-d args] [-t arg] [-g arg] [-q arg]" > 3.4.log &

Params Description:

"[-h] --> Display Help""[-p] --> Project Identifier Number""[-d] --> Comma Spearated Values for Delimiter and Field <delim,field or default> default: _,5""[-t] --> Trimming <nextseq or nova>;""[-g] --> Reference Genome <mm10 or hg38>""[-q] --> Execute atacQC.R script <yes>"

• Create a folder named fastqs and add all the PE fastq files to this folder
• Run the3.4.sh script from the same dir as the fastqs directory

.├──**3.4.sh**├── dedup-BAMS│   ├── PIN.FRIP.multiqc.report_data│   ├── atacQC.out│   ├── featureCounts│   ├── peaks.OUT│   └── tagDirs├── fastQC├──**fastqs**├── primary-BAMS├── trimmed_fastqs└── TrimQC_stats

Tools needed:

1. trim_galore
2. fastqc
3. bwa
4. samtools
5. picard tools
6. homer suite (w/ human and mouse genome config)
7. macs2
8. featureCounts (rsubread)
9. multiqc