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Old 08-20-2013, 10:31 PM   #1
ataraxia
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 (run_RSEM_align_n_estimate.pl) provided by Trinity to estimate abundance using RSEM:

#####
#PBS -S /bin/bash
#PBS -N rsem
#PBS -r y
#PBS -A sf-QCMG
#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

DIR=/directory
SEQDIR=/seqdirectory
OUTDIR=/outdir

run_RSEM_align_n_estimate.pl --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)


Cheers
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