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  • 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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