ARTR-seq data analysis pipeline¶

Summary¶

Pipeline adopted from https://github.com/mingming-cgz/ARTR-seq/ and https://www.encodeproject.org/documents/739ca190-8d43-4a68-90ce-1a0ddfffc6fd/@@download/attachment/eCLIP_analysisSOP_v2.2.pdf

Pipeline has been tested using the ENCODE data from K562: blood_regulome/chenggrp/Projects/Siqi_data/CLIP/RBM9_Public/RBM9_K562

Input format¶

fastq.tsv

This is a tab-seperated-value format file. The 3 columns are: Read 1, Read 2, sample ID.

../../_images/fastq.tsv.png

peakcall.tsv

This is also a tab-seperated-value format file. The 3 columns are: treatment sample ID, control/input sample ID, peakcall ID.

../../_images/peakcall.tsv.png

Usage¶

hpcf_interactive

module load python/2.7.13

HemTools chip_seq_pair --guess_input

run_lsf.py -f fastq.tsv -d peakcall.tsv -p artr_seq -g hg38

Output¶

1. QC report¶

Please check the QC in the html file.

2. called peaks¶