PIPE-CLIP

This is version 1.1.0 Pipeline for CLIP-seq Analysis.

• Galaxy site: the galaxy service is discontinued in 2019.
• Publication: http://genomebiology.com/2014/15/1/R18
• Google Code site: https://code.google.com/p/pipe-clip/

Requirement:

• Python 2.7;
• R 3.0 and above;
• Perl 5 and above;
• Python packages: pysam, pybedtools and ghmm;
• R packages: MASS,VGAM and their dependencies.
• Other packages: HOMER and annotation files

Installation tips:

• Make sure HOMER are in your PATH. You can test this by type "annotatePeaks.pl" from anywhere and you should get help information of this command.

How to use:

• After unzip the package, you cd into the program folder and run PIPE-CLIP by typing:

• python pipeclip.py -i input.bam -o output_prefix -c CLIP_type -l minimum_matchlength -m maximum_mismatchcount -r Remove_PCR_duplicate -M FDR_for_mutations -C FDR_for_clusters -s species

• -i input BAM

• -o output prefix

• -c CLIP type,[0,1,2,3] (0)HITS-CLIP; (1)PAR-4SU; (2)PAR-6SG; (3)iCLIP

• -l minimum match length

• -m maximum mismatch count

• -r method to remove PCR duplicate,[0,1,2] (0)No removal; (1)Remove by read start; (2)Remove by sequence

• -M FDR to get significant mutations

• -C FDR to get enriched clusters

• -s species Here, species might be hg19.

Contact: Zhiqun.Xie@UTSouthwestern.edu