⏳ Quick-ChIP

Quick and easy analysis of ChIP-seq data for visualisation using the UCSC genome browser.

Emily Georgiades, Hughes Lab, July 2021.

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Steps for setup:

1. Create a directory containing:

• yy-mm-dd-experiment-setup.md: file containing info on experimental design and set-up
• jobscript-quick-chip.sh
• paths_to_fastqs.txt: first column specify sample_name (e.g. clone_celltype_condition_rep). Second columns path to directory containing gun-zipped fastqs.

2. Create a public directory where bigwigs will be copied to.

3. Ensure fastqs are gunzipped and named as follows:

Paired-end reads:
sample_name_R1.fastq.gz
sample_name_R2.fastq.gz

Single-end reads:
sample_name.fastq.gz

4. Edit flags in jobscript:

bash quick-chip_withflags.sh -r paired -g genome -t trimming -p public_dir

-r     Specify whether reads are 'single' or 'paired'.
-g    Specify genome build (mm39, mm39-R2, mm39-R1R2 or hg38).
-t     Specify if/which adapters should be trimmed? (no/chip/chipment).
-p    Give path to public directory where bigwigs will be saved (excluding /datashare/).
-h    Display help.

📝  Notes:

Preliminary step is to trim adapters, specifically for NEBNext® Ultra™ / NEBNext® Ultra™ II DNA Library Prep Kits for Illumina®.
Adapter sequence: GAT CGG AAG AGC ACA CGT

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To run the script:
$ sbatch jobscript-quick-chip.sh

To check that it's running:
$ squeue | grep username

To check progress of run (where xxx is jobID):
$ less xxx_quick-chip.out

To cancel the run (where xxx is jobID):
$ scancel xxx