Index of /examples/bioinformatics/bowtie2

[ICO]NameLast modifiedSizeDescription

[PARENTDIR]Parent Directory   -  
[DIR]data/ 2021-04-13 19:42 -  
[DIR]out/ 2021-04-13 19:42 -  
[DIR]qlog/ 2021-04-13 19:42 -  
[DIR]qsub/ 2021-04-13 19:42 -  
[DIR]ref/ 2021-04-13 19:42 -  

RCS Bowtie2 Example

Directory Structure

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:

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:

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

Bowtie2 links

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.