Ok so since I have STAR already installed locally on my scratch space, I’m going to try to do the genome index and alignment using STAR for the Pcli transcriptome. ChatGPT says you can just run it the same way as if you were running a genome index.

#!/bin/bash
#BSUB -J Pcli_transcriptome_STAR_index
#BSUB -q general
#BSUB -P and_transcriptomics
#BSUB -n 8
#BSUB -o Pcli_transcriptome_STAR_index%J.out
#BSUB -e Pcli_transcriptome_STAR_index%J.err
#BSUB -u and128@miami.edu
#BSUB -N

and="/scratch/projects/and_transcriptomics"

/scratch/projects/and_transcriptomics/programs/STAR-2.7.10b/bin/Linux_x86_64_static/STAR \
--runThreadN 16 \
--runMode genomeGenerate \
--genomeDir ${and}/genomes/Pcli \
--genomeFastaFiles ${and}/genomes/Pcli/clean_Pcli_transcriptome_final.fasta

Ok STAR was taking too long so I’m going to try salmon instead.

#!/bin/bash
#BSUB -J Pcli_transcriptome_salmon_index
#BSUB -q general
#BSUB -P and_transcriptomics
#BSUB -n 8
#BSUB -o Pcli_transcriptome_salmon_index%J.out
#BSUB -e Pcli_transcriptome_salmon_index%J.err
#BSUB -u and128@miami.edu
#BSUB -N

and="/scratch/projects/and_transcriptomics"

salmon index -t transcriptome.fasta -i transcriptome_index

Ok the salmon one isn’t running now either. It makes me think that there’s something wrong with the Pcli fasta file or something.