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  • horvathdp
    Member
    • Dec 2011
    • 66
    #1

    more problems with RSEM in Trinity build

    I have down-loaded , and built Trinity, and am still struggling to get my downstream analyses to run.

    here you can see I've ls'd the RSEM file to ensure the executables were present, but they are not found when I try running the program.

    Any thoughts as to why?

    horvathdp@128:/vol-8A5507EB/Trinity/trinityrnaseq_r20131110/util/RSEM_util$ ls
    merge_RSEM_counts_and_labels_single_table.pl Nx_rsem_to_table.pl
    merge_RSEM_frag_counts_single_table.pl run_RSEM_align_n_estimate.pl
    horvathdp@128:/vol-8A5507EB/Trinity/trinityrnaseq_r20131110/util/RSEM_util$ run_RSEM_align_n_estimate.pl --transcripts paradormancy_Trinity_contigs.fasta \ --seqType fq --left 0Hr_1_R1.fq --right 0Hr_1_R2.fq
    bash: run_RSEM_align_n_estimate.pl: command not found
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