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Bioinformatics - Transrate

Instructions on how to run (and, if needed, install a customized version of) Transrate

Transrate is software for de-novo transcriptome assembly quality analysis.

  1. Running Transrate on Thunder
  2. Install customized Transrate on Thunder
Please refer to the CCAST User Guide and the the article Running Bioinformatics Software on HPC Clusters for general information about using CCAST resources and running bioinformatics software on CCAST's HPC clusters.

1. Running Transrate on Thunder


Example: Assemble transcriptomic reads into transcripts


Location: /gpfs1/projects/ccastest/training/examples/Transrate_example


File list

· transrate_job.pbs: job submission script  

· transcripts.fa: reference sequences 

· left.fq: paired-end sequences in fastq format

· right.fq: paired-end sequences in fastq format


Steps

· Copy example directory to your SCRATCH directory

o    cp -r /gpfs1/projects/ccastest/training/examples/Transrate_example $SCRATCH

· Go to the copied directory

o    cd  $SCRATCH/Transrate_example

· Edit the job submission script as needed, then submit the job

o    qsub transrate_job.pbs


2. Install Customized Transrate on Thunder

Warning: This part is intended ONLY for those who want to install and test their own version in their HOME directory.

Summary

(a) Must keep the directory structure of the package intact, because Transrate comes packaged with its binary dependencies;

(b) Need to install BLAST+ if using reference-based metrics.

Details

In the following pages, we assume that you want to install the software in a directory named “SOFTWARE” inside your HOME directory on the CCAST’s Thunder cluster. “USERNAME is your username on Thunder.


(a) Install

· Go to your software directory: 

o    "cd /gpfs1/home/USERNAME/SOFTWARE

· Download and unzip Transrate: 

o    "wget https://bintray.com/artifact/download/blahah/generic/transrate-1.0.3-linux-x86_64.tar.gz

o    "tar -xzvf transrate-1.0.3-linux-x86_64.tar.gz"

(b) Test

· Go to the scratch directory: 

o    "cd /gpfs1/scratch/USERNAME

· Make and go into test directory: 

o    "mkdir Transrate_example"

o    "cd Transrate_example"

· Download data file, unzip, and thereafter delete the original compressed file for clarity:

o    "wget https://bintray.com/artifact/download/blahah/generic/example_data.tar.gz

o    "tar --strip 1 -zxvf example_data.tar.gz && rm example_data.tar.gz"

· Write and submit the job 

o    "qsub transrate_job.pbs

--------------- transrate_job.pbs -----------------

#!/bin/bash

#PBS -q default

#PBS -N Transrate_test

##change mem, ncpus, and walltime as needed:

#PBS -l select=1:mem=10gb:ncpus=4

#PBS -l walltime=1:00:00

## Replace “x-ccast-prj” with “x-ccast-prj-[your project group name here]”

#PBS -W group_list=x-ccast-prj

cd $PBS_O_WORKDIR

Add Transrate Binaries to $PATH

export PATH=$PATH:/gpfs1/home/USERNAME/SOFTWARE/transrate-1.0.3-linux-x86_64

##runnung Transrate

transrate --assembly transcripts.fa --left left.fq --right right.fq \

--threads $NCPUS

exit 0

 

See Also:




Keywords:ccast, hpc, thunder, bioinformatics, transrate   Doc ID:108085
Owner:Liu Y.Group:IT Knowledge Base
Created:2020-12-27 10:17 CSTUpdated:2020-12-29 01:09 CST
Sites:IT Knowledge Base
CleanURL:https://kb.ndsu.edu/transrate
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