#!/bin/tcsh

#BSUB -J starindices_Soy_CCV-1 #job name

#BSUB -n 12 #number of nodes

#BSUB -W 2:0 #time for job to complete

#BSUB -o starindices.out.%J #output file

#BSUB -e starindices.err.%J #error file

# For running star to generate genome index

# Run in working directory /share/bitcpt/S23/cacofre/Portfolio

# Must run this in working directory with subdirectory named starindices/

set STAR=/usr/local/usrapps/bitcpt/star/bin/STAR

set IN=/share/bitcpt/S23/referenceGenomes/Portfolios/Glycine_max_Wm82-ISU01_v2/

${STAR} --runThreadN 12 --runMode genomeGenerate --genomeSAindexNbases 13 --genomeDir starindices/ --genomeFastaFiles ${IN}/glyma.Wm82_ISU01.gnm2.JFPQ.genome_main.fna --sjdbGTFfile ${IN}/glyma.Wm82_ISU01.gnm2.ann1.FGFB.gene_models_main.AGAT.gtf --sjdbOverhang 100

Set Variables

set STAR=/usr/local/usrapps/bitcpt/star/bin/STAR

Command set defines variable STAR to be (=) the path to the user maintained software

set IN=/share/bitcpt/S23/referenceGenomes/Soy/Glycine_max_Lee_v2/

Command set defines variable IN to be (=) the path to the reference genome

Command Options Breakdown

${STAR}

this is the command to run star software

It calls the preset variable 'STAR'

--runThreadN 12 

set the number of threads, must match #BSUB -n value. Hazel maximum is 12!

--runMode genomeGenerate 

STAR can do genome indexing and alignment. Here we're telling STAR that we want to index the genome. 

--genomeSAindexNbases 13 

• default: 14 

• int:  length (bases) of the SA pre-indexing string.  Typically between 10 and 15.  Longer strings will use much more memory, but allow faster searches.  For small genomes, the parameter –genomeSAindexNbases must be scaled down to min(14, log2(GenomeLength)/2 - 1). 

• set to star manual's recommendation for Soy genome size 

• Wolframalpha link shows math where ~1015016903 is Soy genome size: 

  • The theoretical genome length of Soy is 1.1 Gb, so log2(1015016903)/2-1 = ~13.9 , always best to round (down) to the nearest whole number (13).

--genomeDir starindices/ 

Tell STAR where to write the output

--genomeFastaFiles ${IN}/glymaa.Lee.gnm2.K7BV.genome_main.fna

Tell STAR where the genome assembly file(s) are

--sjdbGTFfile ${IN}/glyma.Lee.gnm2.ann1.1FNT.gene_models_main.AGAT.gtf 

Tell STAR where the annotation file is

--sjdbOverhang 100

Length of RNA-seq reads - 1. However, from the manual: In most cases, the default value of 100 will work as well as the ideal value. 

If the job is successfully completed, no message will appear when using the command: "more starindices.err.XXXXX", whereas the "succesfully completed" message will appear when checking the starindices.out.XXXXX file.