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README.md

PIPE-CLIP

This is version 1.1.0 Pipeline for CLIP-seq Analysis.

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

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