Final Student Portfolio

Overview

In this section, I am going to be using STAR to incorporate my processed fasta files into a program that checks for overlaps and use them as a reference to form longer sequences. These build from reads, into contigs, and ultimately into scaffolds. This allows us to speed up the alignment process by finding the overlapping regions in comparison to the reference genome.

What is STAR?

Spliced Transcripts Alignment to a Reference, STAR, is an aligner program that is designed to specifically address many of the challenges of RNA-seq data mapping using a strategy that is also spliced aware.

Indexing Cherry Tomato

#Copy the index script into the Portfolio directory

#I am going to call my script files moving forward as Cher.

#directory: /share/bitcpt/Fall2022/UnityID/Portfolio

cp /share/bitcpt/Fall2022/mmohamm8/Tom/Tom.starindex.sh Cher.starindex.sh

ll #to make sure 'Cher.starindex.sh' is located in the Portfolio directory

#To look at the content of the index script

more Cher.starindex.sh

#To edit the script

vi Cher.starindex.sh #press I to edit, "esc" to stop editing, and type ":wq" to exit the file.

#Cherry tomato index script, make sure to have the starindices directory in the Portfolio directory

#!/bin/tcsh

#BSUB -J starindices_Cher_AfiqTom #job name

#BSUB -n 10 #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/Fall2022/UnityID/Portfolio/Tom-Cherry

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

module load conda

conda activate /usr/local/usrapps/bitcpt/star

set IN=/share/bitcpt/Fall2022/referenceGenomes/Solanum_lycopersicum/Portfolio/Tom-Cherry

STAR --runThreadN 10 --runMode genomeGenerate --genomeSAindexNbases 13 --genomeDir starindices --genomeFastaFiles ${IN}/Tom-Cherry_assembly.fasta --sjdbGTFfile ${IN}/Tom-Cherry.agat.gtf --sjdbOverhang 100

# I used the overhang default 100 and it worked!