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,pybedtoolsandrpy2. (Python packages will be installed automaticallly) -
R >=3.0;
-
R packages:
MASS,VGAMand 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
-iinput BAM-tcontrol BAM-ooutput prefix-cCLIP type,[0,1,2,3] (0)HITS-CLIP; (1)PAR-4SU; (2)PAR-6SG; (3)iCLIP-rmethod to remove PCR duplicate,[0,1,2] (0)No removal; (1)Remove by read start; (2)Remove by sequence-lminimum match length-mmaximum mismatch count-MFDR to get significant mutations-CFDR to get enriched clusters-sspecies. (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
1 maintainer
Metadata
1 maintainer
Release files for pipeclip 2.0.10
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