Go Back   SEQanswers > Applications Forums > RNA Sequencing

Similar Threads
Thread Thread Starter Forum Replies Last Post
RSEM: has anyone tried this? ejcho82 RNA Sequencing 2 09-14-2019 12:08 PM
Input file format for RSEM edge Bioinformatics 1 09-20-2012 06:33 AM
question about python module pyvcf andylai Bioinformatics 1 09-18-2012 07:58 AM
RSEM expected counts question tboothby Bioinformatics 2 01-26-2012 05:45 AM
RSEM vs. samtools vs. other for expression? yeaman Bioinformatics 1 12-01-2011 09:52 AM

Thread Tools
Old 08-20-2013, 10:31 PM   #1
Junior Member
Location: Australia

Join Date: Feb 2013
Posts: 7
Default question about the RSEM module within trinity

Hi all,
I am running a PBS script on our server using the perl script ( provided by Trinity to estimate abundance using RSEM:

#PBS -S /bin/bash
#PBS -N rsem
#PBS -r y
#PBS -l select=1:ncpus=8:mem=36g:NodeType=large
#PBS -l walltime=6:00:00

module load trinity
module load bowtie/2.1.0
module load tophat/2.0.8

OUTDIR=/outdir --seqType fq --SS_lib_type RF --left $SEQDIR/ipsc1.fq --right $SEQDIR/ipsc2.fq --thread_count 8 --prefix $OUTDIR/ipsc --transcripts $DIR/trinity/output3/Trinity.fasta


I was just wandering if anyone knew if there was an option to redirect the TRANS.* files created (which correspond to the reference_name files produced by RSEM) to a specific location instead of my home directory (default)

ataraxia is offline   Reply With Quote

pbs, rsem, trinity

Thread Tools

Posting Rules
You may not post new threads
You may not post replies
You may not post attachments
You may not edit your posts

BB code is On
Smilies are On
[IMG] code is On
HTML code is Off

All times are GMT -8. The time now is 12:29 AM.

Powered by vBulletin® Version 3.8.9
Copyright ©2000 - 2020, vBulletin Solutions, Inc.
Single Sign On provided by vBSSO