File: run_Schizo_TrinityGG.sh

package info (click to toggle)
trinityrnaseq 2.11.0%2Bdfsg-6
  • links: PTS, VCS
  • area: main
  • in suites: bullseye
  • size: 417,528 kB
  • sloc: perl: 48,420; cpp: 17,749; java: 12,695; python: 3,124; sh: 1,030; ansic: 983; makefile: 688; xml: 62
file content (5 lines) | stat: -rwxr-xr-x 483 bytes parent folder | download | duplicates (4) 
1
2
3
4
5
 
#!/bin/bash -ve

../../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 4 --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 2 --output test_Schizo_GG_outdir
# adding some extra params just to make sure all opts get forwarded on to where they're needed.