Index of /examples/bioinformatics/basic

Name	Last modified	Size

Parent Directory		-
,	2021-07-14 10:12	3.5K
bowtie2_basic.qsub	2021-07-14 10:23	818
bowtie2_basic_exampl..>	2021-07-14 10:27	6.1K
bowtie2_example_SRR0..>	2021-07-14 10:27	1.4G
data/	2021-07-14 10:12	-
ref/	2021-07-14 10:20	-

RCS Bioinformatics Basic Examples

Directory Structure

data/ - Directory to store sample data
ref/ - Directory to store reference genome data
bowtie2_basic.qsub - Batch script example
bowtie2_basic_example.o7690290 - Batch job log file provided as an example
bowtie2_example_SRR030257.sam - Example sam output

Notes

To view available bowtie2 versions on SCC, execute:

[scc1 ] module avail bowtie2

To run bowtie2 tools at the command line:


[scc1 ] module load  bowtie2/2.4.2 # always attach the version of the software
[scc1 ] cd ref
[scc1 ] bowtie2-build NC_012967.1.fasta NC_012967.1      # build index
[scc1 ] cd ..
[scc1 ] bowtie2 -t -x ref/NC_012967.1 -1 data/SRR030257_1.fastq -2 data/SRR030257_2.fastq -S bowtie2_example_SRR030257.sam  # align sample sequence data against reference

To submit a job:
[scc1 ] qsub bowtie2_basic.qsub

Online Resources

Contact Information

Research Computing Services: help@scc.bu.edu

Note: RCS example programs are provided "as is" without any warranty of any kind. The user assumes the intire risk of quality, performance, and repair of any defect. You are welcome to copy and modify any of the given examples for your own use.