PIPE-CLIP

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.

Footnote

Cite:

• Chen, B., Yun, J., Kim, M.S. et al. PIPE-CLIP: a comprehensive online tool for CLIP-seq data analysis. Genome Biol 15, R18 (2014). https://doi.org/10.1186/gb-2014-15-1-r18