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test3 - q1_salmon

STAR - index and map

Indexing failed with 2 cores, get 3:

qsub -I -A ACF-UTK0138 -q debug -l walltime=1:00:00,nodes=1:ppn=3,advres=epp622.13776065

Index command:

/lustre/haven/proj/UTK0138/software/STAR-2.7.6a/bin/Linux_x86_64/STAR \
--runMode genomeGenerate \
--genomeDir STAR_idx \
--genomeFastaFiles Ppersica_298_v2.0.fa \
--runThreadN 1 \
--sjdbGTFfile Ppersica_298_v2.1.gene_exons.gff3 \
--sjdbGTFtagExonParentTranscript Parent \
--sjdbOverhang 50

Make filenames file:

ls ../*fq > filenames.txt

Run qsub task array job:

#PBS -S /bin/bash
#PBS -A ACF-UTK0138
#PBS -l nodes=1:ppn=2,walltime=01:00:00
#PBS -l advres=epp622.13776065
#PBS -N rna-map
#PBS -m abe
#PBS -M yourusername@utk.edu
#PBS -t 1-6

cd $PBS_O_WORKDIR

infile=$(sed -n -e "${PBS_ARRAYID} p" filenames.txt)

samplename=$(basename $infile | sed 's/.fq//')

/lustre/haven/proj/UTK0138/software/STAR-2.7.6a/bin/Linux_x86_64/STAR \
--genomeDir ../STAR_idx \
--readFilesIn $infile \
--runThreadN 2 \
--outFileNamePrefix $samplename \
--outSAMtype BAM SortedByCoordinate

Count:

module load htseq
module load pysam

for f in *bam
do
    samplename=$(basename $f | sed 's/Aligned.sortedByCoord.out.bam//g')
    echo $base
    htseq-count \
    --format=bam \
    --order=pos \
    --stranded=no \
    --type=gene \
    --idattr=ID \
    $f \
    ../Ppersica_298_v2.1.gene_exons.gff3 \
    >${samplename}.counts.txt
done

Salmon

Index the transcripts:

/lustre/haven/proj/UTK0138/software/salmon-latest_linux_x86_64/bin/salmon \
index \
-t Ppersica_298_v2.1.transcript.fa \
-i salmon_idx

Map:

#PBS -S /bin/bash
#PBS -A ACF-UTK0138
#PBS -l nodes=1:ppn=2,walltime=00:20:00
#PBS -l advres=epp622.13776065
#PBS -N salmon-map
#PBS -m abe
#PBS -M mstaton1@utk.edu
#PBS -t 1-6

cd $PBS_O_WORKDIR

infile=$(sed -n -e "${PBS_ARRAYID} p" filenames.txt)

samplename=$(basename $infile | sed 's/.fq//')

/lustre/haven/proj/UTK0138/software/salmon-latest_linux_x86_64/bin/salmon \
quant \
-i ../salmon_idx \
-l A \
-r $infile \
--validateMappings \
-p 2 \
-o ${samplename}_transcripts_quant