scripts/STAR_commands.txt

Version 1

#SUSPHIRE SxP Nb datasets mapping to the new genome

cd /DATA/mojcaj/STAR_mapping

#ulimit default 1024

ulimit -n 10000


#unzip genome files

gzip -d ./NbAUSv1.0_2019-11-29.fasta.gz
gzip -d ./NbAUSv1.0_AUGUSTUS-genes_2019-12-02.gff3.gz

# generate genome index
STAR \
--runThreadN 8 \
--runMode genomeGenerate \
--genomeDir ./index \
--genomeFastaFiles ./NbAUSv1.0_2019-11-29.fasta \
--sjdbGTFfile ./NbAUSv1.0_AUGUSTUS-genes_2019-12-02.gff3 \
--sjdbGTFtagExonParentTranscript ID \
--sjdbOverhang 100 \
--limitGenomeGenerateRAM 50000000000

# map reads
STAR --genomeLoad LoadAndExit --genomeDir ./index

for i in $(ls /DATA/mojcaj/CoExpNetViz_data/PE/ | sed s/_[12].fastq.gz// | sort -u)
do  STAR \
	--genomeDir ./index \
	--quantMode GeneCounts \
	--runThreadN 8 \
	--readFilesIn /DATA/mojcaj/CoExpNetViz_data/PE/${i}_1.fastq.gz,/DATA/mojcaj/CoExpNetViz_data/PE/${i}_2.fastq.gz \
	--readFilesCommand pigz -c -d \
	--outFileNamePrefix /DATB/mojcaj/SxP_CoExp_STAR_$i. \
	--outFilterMultimapNmax 4 \
	--outFilterMismatchNoverReadLmax 0.05 \
	--outSAMtype BAM SortedByCoordinate \
	--quantTranscriptomeBan Singleend \
	--limitBAMsortRAM 50000000000
done


for i in $(ls /DATA/mojcaj/CoExpNetViz_data/SE/ | sed s/.fastq.gz// | sort -u)
do  STAR \
	--genomeDir ./index \
	--quantMode GeneCounts \
	--runThreadN 8 \
	--readFilesIn /DATA/mojcaj/CoExpNetViz_data/SE/${i}.fastq.gz \
	--readFilesCommand pigz -c -d \
	--outFileNamePrefix /DATB/mojcaj/SxP_CoExp_STAR_$i. \
	--outFilterMultimapNmax 4 \
	--outFilterMismatchNoverReadLmax 0.05 \
	--outSAMtype BAM SortedByCoordinate \
	--quantTranscriptomeBan Singleend \
	--limitBAMsortRAM 50000000000
done










STAR --genomeLoad Remove --genomeDir ./index

gzip ./NbAUSv1.0_2019-11-29.fasta
gzip ./NbAUSv1.0_AUGUSTUS-genes_2019-12-02.gff3