pipeclip 2.0.1

PIPELINE FOR CLIP SEQ DATA

PIPE-CLIP

Pipeline for CLIP-seq Analysis. This is a fork version (2.0.0) of PIPE-CLIP.

Requirement:

• Python >=3.6;
• R >=3.0
• Perl >=5.0
• Python packages: pysam, pybedtools and ghmm;
• R packages: MASS, VGAM and their dependencies.
• 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 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. (species might be hg19, mm10, mm9.)

Footnote

• Contact: [e-mail]
• Publication: http://genomebiology.com/2014/15/1/R18
• Google Code site: https://code.google.com/p/pipe-clip/