Index of /examples/bioinformatics/bowtie2

Name	Last modified	Size

Parent Directory		-
data/	2021-04-13 19:42	-
out/	2021-04-13 19:42	-
qlog/	2021-04-13 19:42	-
qsub/	2021-04-13 19:42	-
ref/	2021-04-13 19:42	-

RCS Bowtie2 Example

Directory Structure

data - dedicated folder to store download sequence data.
data/SRR030257_1.fastq - pair-end read 1 sample data.
data/SRR030257_2.fastq - pair-end read 2 sample data.
ref - dedicated folder to store all input files.
ref/NC_012967.1.fasta - reference genome for E. Coli B strain REL606.
out - dedicated folder to organize output files.
qsub - dedicated folder to store all qsub scripts.
qsub/bowtie2_job.qsub - batch script example
qlog -d dedicated folder to store all qsub output logs.

Notes

1. To view all available BOWTIE2 versions on SCC, execute:


    [scc1 ] module avail bowtie2

2. Before run any BOWTIE2 ulitilies, first to load bowtie2 module to make them available:


    [scc1 ] module load bowtie2/2.4.2

Command Line Examples

Ex1: Get Help on bowtie2 command


    [scc1 ]  ls $SCC_BOWTIE2_BIN # use this command to list all available command
    [scc1 ]  bowtie2 -h # print help page for bowtie2 command
    [scc1 ]  bowtie2-build -h # print help page for bowtie2-build command
    [scc1 ]  bowtie2-inspect -h # print help page for bowtie2-inspect command

There are 9 total binary files, 3 sets for each group in the $SCC_BOWTIE2_BIN directory:

bowtie2-build - wrapper script for bowtie2-build-l and bowtie2-build-s
bowtie2-align-l - actual script called by bowtie2-build for building large reference index, result file will have .bt2l postfix
bowtie2-align-s - actual script called by bowtie2-build for building small reference index, result file will have .bt2 postfix
bowtie2-inspect - wrapper script for bowtie2-inspect-l and bowtie2-inspect-s
bowtie2-inspect-l - actual script called by bowtie2-inspect for long bowtie2 index files
bowtie2-inspect-s - actual script called by bowtie2-inspect for short bowtie2 index files
bowtie2 - wrapper script for bowtie2-align-l and bowtie2-align-s
bowtie2-align-l - actual script called by bowtie2 for long read alignment
bowtie2-align-s - actual script called by bowtie2 for short read alignment

Ex2: Build Index for the example genome:


    [scc1 ]  bowtie2-build ref/NC_012967.1.fasta ref/NC_012967.1   # build index for E. coli reference and put the index files in the same directory as reference sequence
    [scc1 ]  ls -l ref  # check ref/ and see the new index files generated

* the command output can be seen in out/bowtie2-index.out

Ex3: Examine the index files using bowtie2-inspect:


    [scc1 ] bowtie2-inspect --summary ref/NC_012967.1  # print summary
    [scc1 ] bowtie2-inspect --names ref/NC_012967.1  # print reference name

* Please note - in all bowtie2 commands, where index is needed, only give the basename for the index file.
The screen output for the above commands is recorded in out/bowtie2-inspect.out.

Ex4: Run sequence alignment using bowtie2:


    [scc1 ] bowtie2 -t -x ref/NC_012967.1 -1 data/SRR030257_1.fastq -2 data/SRR030257_2.fastq -S data/SRR030257.sam #align the pair end reads for SRR030257, and store result in SAM format in the same data/ directory
    [scc1 ] head data/SRR030257.sam  # print the first several lines of output sam

The screen output for the above commands is recorded in out/bowtie2.out.

Batch Job Example:

You can write a qsub script to combine many operations together, including adding some post processing using samtools/bcftoos. An example qsub is in qsub/bowtie2_job.qsub


    [scc1 ] cd qsub # get into the qsub script location
    [scc1 ] qsub bowtie2_job.qsub

After the above job's completion, there will be two files in qlog/ looks like:

qlog/bowtie2_example.oxxxxxxx
qlog/bowtie2_example.poxxxxxxx # 'xxxxxxx' stands for job number

And the output files generated from this job are in data/, start with 'bowtie2_example_SRR030257.xxx

Bowtie2 links

Official Bowtie2 Manual

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.