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How to run BLAT on clusters



Notes:

Human Genome
1. Data for each chromosome (from NCBI) is located at /pub1/ftp-ncbi-blast/genomes/H_sapiens directory
2. BLAT is installed at /shr/home/source/blat
3. The 2bit formatted entire human genome data (in order to run UCSC blat) is located at /pub1/ucsc-genome/hg18.2bit
4. To speed up your search, the blat server for human chromosomes has been started at node n1 with port 17779


Mouse Genome
1. Data for each chromosome (from NCBI) is located at /pub1/ftp-ncbi-blast/genomes/M_musculus directory
2. BLAT is installed at /shr/home/source/blat
3. The 2bit formatted entire mouse genome data (in order to run UCSC blat) is located at /pub1/ucsc-genome/mm8.2bit
4. To speed up your search, the blat server for mouse chromosomes has been started at node n1 with port 17780


A much more powerful web portal will be available in Feb, 2008, email notification will be broadcasted.

Step 1: Please read "how to setup your working environment" and do the following:

a. Include the sentence of "module load blat/default" in the module-loading blocks in your .bashrc file
b. Type ". .bashrc" in your terminal, and then type "module list or type "which blat" in your terminal again, you shall see:

[testy@n137 ~]$ . .bashrc
[testy@n137 ~]$ module list
Currently Loaded Modulefiles:
   1) blat/default
[testy@n137 ~]$ which blat
/source/blat/bin/x86_64-redhat-linux-gnu/blat

#!/bin/bash

# enable your environment, which will use .bashrc configuration in your home directory
#BSUB -L /bin/bash

# the name of your job showing on the queue system
#BSUB -J blattest

# the queue that you will use, the example here use the queue called "normal"
# please use bqueus command to check the available queues
#BSUB -q normal


# the system output and error message output, %J will show as your jobID
#BSUB -o %J.out
#BSUB -e %J.err

#the CPU number that you will collect
#BSUB -n 1

#when job finish that you will get email notification
#BSUB -u yourID@partners.org
#BSUB -N


#enter your working directory, change to your own dir
cd /shr/home/$USER/blat_example


#Finally, Start the blat, this is to search against mouse, change the port number to 17779 to search again human

gfClient n1 17780  / testmouse.fas  outputtest.psl -out=blast -minScore=30 -minIdentity=90 -q=dna

 [testy@n137 ~] bsub < blat.lsf