Index of /examples/bioinformatics/bowtie2

Icon  Name                    Last modified      Size  Description
[DIR] Parent Directory - [   ] bowtie2_st_job.qsub 20-Nov-2017 13:58 419 [   ] bowtie2_mt_job.qsub 21-Nov-2017 14:26 936

Bowtie2 package example

There are two example scripts provided here:

bowtie2_st_job.qsub
- the simple single thread bowtie job

bowtie2_mt_job.qsub
- the multi-thread job taking advantage of bowtie2's parallel support for better performance. It is recommended to use bowtie2 this way when dealing with large alignment job, such as build hg38 human genome index. Please note, the E.Coli reference is used in the example, for demo purpose.

To run bowtie at the command line:

scc4% module load intel/2016
scc4% module load bowtie2/2.3.3.1_intel-2016


scc4% bowtie2-build $SCC_BOWTIE2_EXAMPLES/reference/lambda_virus.fa lambda_virus

scc4% bowtie2 -x lambda_virus -U $SCC_BOWTIE2_EXAMPLES/reads/reads_1.fq -S eg1.sam


To submit a job, execute command:
scc4% qsub -P my_project my_bowtie2_job.qsub

Manual for Bowtie2: http://bowtie-bio.sourceforge.net/bowtie2/manual.shtml

NOTES worth to point out:

a. Bowtie 2 indexes work only with v2 (not v1). Likewise for v1 indexes. If the wrong version of index is used when using bowtie2 aligner, it could be the cause of many weird memory segmentation errors observe.

b. some commonly used reference indexes are already built on SCC, they are under $SCC_BOWTIE2_REF directory. Please take a look at it and maybe it could save you some time to build the reference indexes by yourself.