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Wednesday, December 7, 2016
CREST (Clipping Reveals Structure) is a new algorithm for detecting genomic structural variations at base-pair resolution using next-generation sequencing data. Publication: http://www.ncbi.nlm.nih.gov/pubmed/21666668
To run this software interactively in a Linux environment run the commands:
module load crest
Note: a standard workflow with CREST requires a BLAT server. Detailed instructions are in the README file distributed with the software (e.g., /soft/crest/1.0/bin/README). Your jobs should contain the following workflow:
# load the appropriate modules
module load crest
# Using the blat utility faToTwoBit program, convert the genome file to
# a 2bit representation suitable for the gfServer
faToTwoBit genome.seq.fasta genome.seq.2bit
# start up the server
gfServer start localhost 50000 /absolute/path/genome.seq.2bit &
#sleep until you notice "Server ready for queries!", then run the CREST.pl
# Gather up the soft clipped positions in your BAM alignment file.
# NOTE: the BAM file must be sorted and indexed (e.g., using samtools)
# prior to proceeding.
extractSClip.pl -i your_mapping.bam --ref_genome genome.seq.fasta
# If you are doing contrastative projects (e.g., tumors and normals)
# the CREST README has some additional optional steps
# Now run the SV detection script.
# There are other options you can explore by simply typing 'CREST.pl'
# or checking the README with the distribution. But here are the basics.
CREST.pl -f your_mapping.bam.cover -d your_mapping.bam \
--ref_genome genome.seq.fasta -t /absolute/path/genome.seq.2bit \
--blatserver localhost --blatport 50000 >& crest_out.log
# cleanup server
gfServer stop localhost 50000