CREST

To run this software interactively in a Linux environment run the commands:

module load crest
CREST.pl

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

Homepage:http://www.stjuderesearch.org/site/lab/zhang