Pipeline for CLIP-seq Analysis. This is a fork version (2.0.x) of PIPE-CLIP.
-
Python >=3.6;
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Python packages:
pysam
,pybedtools
andrpy2
. (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.
pip install pipeclip
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.
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