BitSeq

Overview

BitSeq (Bayesian Inference of Transcripts from Sequencing Data) is an application for inferring expression levels of individual transcripts from sequencing (RNA-Seq) data and estimating differential expression (DE) between conditions.

Version 0.7.0 is installed on the CSF. It was compiled with GNU compilers 4.4.6 and the default settings in the makefile.

Restrictions on use

Any CSF user may access the software as it is open source under the Artistic License/GPL.

Set up procedure

To access the software you must first load the modulefile:

module load apps/gcc/bitseq/0.7.0

Running the application

Bitseq should not be run on the login node. You should create a jobscript containing the appropriate batch system options and Bitseq commands and then submit the jobscript using:

qsub jobscript_name

It may be necessary to use other applications in conjunction with Bitseq.

Panagiotis Papastamoulis, from FLS, has very kindly provided some documentaion illustrating how to use Bitseq on the CSF, in conjunction with other tools and including example jobscripts.

Further info

• BitSeq
• Related applications available on the CSF:
• Bowtie2
• Samtools

Updates

None.