This is version 1.1.0 Pipeline for CLIP-seq Analysis.
- Galaxy site: the galaxy service is discontinued in 2019.
- Publication: http://genomebiology.com/2014/15/1/R18
- Google Code site: https://code.google.com/p/pipe-clip/
- Python 2.7;
- R 3.0 and above;
- Perl 5 and above;
- Python packages: pysam, pybedtools and ghmm;
- R packages: MASS,VGAM and their dependencies.
- Other packages: HOMER 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 Here, species might be hg19.