bixbeta / trex

RNA-seq, smRNA-seq, scRNA-seq & ATAC-seq workflows for @Cornell-Trex

beta6.sh <- RNA-seq workflow

Dependencies:

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

3.4.sh <- ATAC-seq workflow

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 the 3.4.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