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PIPE-CLIP

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Pipeline for CLIP-seq Analysis. This is a fork version (2.0.x) of PIPE-CLIP.

Requirement:

  • Python >=3.6;

  • Python packages: pysam, pybedtools and rpy2. (Python packages will be installed automaticallly)

  • R >=3.0;

  • R packages: MASS, VGAM and their dependencies. (R packages will be installed automatically)

  • Perl >=5.0

  • Other packages: HOMER (annotatePeaks.pl) and annotation files

    • 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 install:

pip install pipeclip

How to use:

pipeclip -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
  • -t control BAM
  • -o output prefix
  • -c CLIP type,[0,1,2,3] (0)HITS-CLIP; (1)PAR-4SU; (2)PAR-6SG; (3)iCLIP
  • -r method to remove PCR duplicate,[0,1,2] (0)No removal; (1)Remove by read start; (2)Remove by sequence
  • -l minimum match length
  • -m maximum mismatch count
  • -M FDR to get significant mutations
  • -C FDR to get enriched clusters
  • -s species. (species might be hg19, mm10, mm9.) Leave blank to skip annotation step.

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