Index of /examples/bioinformatics/tophat

Name	Last modified	Size

Parent Directory		-
ref/	2021-04-16 17:39	-
qsub/	2021-04-16 17:38	-
qlog/	2021-04-16 17:38	-
out/	2021-04-16 17:38	-
data/	2021-04-16 17:38	-

RCS TopHat Example

Directory Structure

data - dedicated folder to store download sequence data.
data/reads_1.fq - pair-end read 1 sample data.
data/reads_2.fq - pair-end read 2 sample data.
ref - dedicated folder to store all input files.
ref/test_ref.fa - reference genome for test purpose, grabbed from tophat package.
out - dedicated folder to organize output files.
qsub - dedicated folder to store all qsub scripts.
qsub/tophat_job.qsub - batch script example
qlog -d dedicated folder to store all qsub output logs.

Notes

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


    [scc1 ] module avail tophat

2. Before run tophat, first to load tophat and bowtie2 module to make the command available:


    [scc1 ] module load bowtie2/2.4.2  # though tophat can work with old bowtie (bowtie1), it's rare usage. So suggest to load bowtie2 as the backend aligner for tophat
    [scc1 ] module load tophat/2.1.1

Command Line Examples

Ex1: run tophat on single end reads, in the example, we use '--num-threads 2' to specify using two cores:


    [scc1 ]  tophat --num-threads 2 --no-coverage-search -o out/tophat_se ref/test_ref data/reads_1.fq

* the screen output from the above command can be seen in out/tophat_se.out ** and the tophat mapping result is put in out/tophat_se.

Ex2: run tophat on pair end reads, using two cores:


    [scc1 ]  tophat --num-threads 2 --no-coverage-search -o out/tophat_pe ref/test_ref data/reads_1.fq data/reads_2.fq

* the screen output from the above command can be seen in out/tophat_pe.out ** and the tophat mapping result is put in out/tophat_pe/.

Batch Job Example:

You can write a qsub script to combine many operations together, including adding some pre- and/or post-processing using other tools. An example qsub is in qsub/tophat_job.qsub


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

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

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

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

TopHat links

TopHat Manual Page

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.