File: run_Schizo_TrinityGG.sh

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trinityrnaseq 2.15.2%2Bdfsg-1
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#!/bin/bash -ve

CPU=$(nproc || sysctl -n hw.physicalcpu)

../../Trinity --seqType fq --left top100k.Left.fq.gz --right top100k.Right.fq.gz --genome top100k.genome.gz --genome_guided_use_bam SP2.chr.bam --JM 1G --CPU ${CPU} --genome_guided_max_intron 1000 --SS_lib_type RF --bfly_opts "--no_path_merging --triplet_strict -R 1 -O 10 --edge-thr=0.04" --genome_guided_sort_buffer 6G --genome_guided_CPU $((${CPU} / 2)) --output test_Schizo_GG_outdir
# adding some extra params just to make sure all opts get forwarded on to where they're needed.