Index of /examples/bioinformatics/bowtie

Icon  Name                    Last modified      Size  Description
[DIR] Parent Directory - [DIR] indexes/ 06-Mar-2015 16:31 - [   ] bowtie_job.qsub 06-Mar-2015 16:37 288

Bowtie package example

To run bowtie at the command line:

scc4% module load bowtie/1.1.1

scc4% bowtie -a -v 2 $SCC_BOWTIE_BIN/indexes/e_coli --suppress 1,5,6,7 -c ATGCATCATGCGCCAT
scc4% bowtie $SCC_BOWTIE_BIN/indexes/e_coli $SCC_BOWTIE_BIN/reads/e_coli_1000.fq
scc4% bowtie -c s_cerevisiae ATTGTAGTTCGAGTAAGTAATGTGGGTTTG


To submit a job, execute command:
scc4% qsub -P my_project bowtie_job.qsub

Manual for Bowtie:
http://bowtie-bio.sourceforge.net/manual.shtml