ulimit -n 10000


mkdir ../output/PGSC/
mkdir ../output/gff-merged/
mkdir ../output/Desiree/

# stCuSTr-D_tr_representatives.fasta
# Desiree STAR PE mapping
STAR \
--runMode alignReads \
--runThreadN 30 \
--genomeDir ../intermediate/Desiree/ \
--readFilesIn \
../input/SRR10416847_1.fastq \
../input/SRR10416847_2.fastq \
--outFileNamePrefix ../output/Desiree/ \
--outSAMtype BAM SortedByCoordinate

# samtools --version
## samtools 1.9-210-g72d140b
## Using htslib 1.9-437-g71d8683
## Copyright (C) 2019 Genome Research Ltd.


#index bam file
samtools index ../output/Desiree/Aligned.sortedByCoord.out.bam



# StPGSC4.04n_seq_2_PGSC-t-rep_ITAG-cds_gff-2019-04-23.fasta
# Desiree STAR PE mapping
STAR \
--runMode alignReads \
--runThreadN 30 \
--genomeDir ../intermediate/gff-merged/ \
--readFilesIn \
../input/SRR10416847_1.fastq \
../input/SRR10416847_2.fastq \
--outFileNamePrefix ../output/gff-merged/ \
--outSAMtype BAM SortedByCoordinate

samtools index ../output/gff-merged/Aligned.sortedByCoord.out.bam



# PGSC_DM_v3.4_transcript-update_representative.fasta
# Desiree STAR PE mapping
STAR \
--runMode alignReads \
--runThreadN 30 \
--genomeDir ../intermediate/PGSC/ \
--readFilesIn \
../input/SRR10416847_1.fastq \
../input/SRR10416847_2.fastq \
--outFileNamePrefix ../output/PGSC/ \
--outSAMtype BAM SortedByCoordinate

samtools index ../output/PGSC/Aligned.sortedByCoord.out.bam


mv ../output/PGSC/ ../output/PGSC_SRR10416847/
mv ../output/gff-merged/ ../output/gff-merged_SRR10416847/
mv ../output/Desiree/ ../output/Desiree_SRR10416847/

mkdir ../output/PGSC_SRR10416848/
mkdir ../output/gff-merged_SRR10416848/
mkdir ../output/Desiree_SRR10416848/

mkdir ../output/PGSC_SRR10416849/
mkdir ../output/gff-merged_SRR10416849/
mkdir ../output/Desiree_SRR10416849/

mkdir ../output/PGSC_drought123/
mkdir ../output/gff-merged_drought123/
mkdir ../output/Desiree_drought123/



# stCuSTr-D_tr_representatives.fasta
# Desiree STAR PE mapping
STAR \
--runMode alignReads \
--runThreadN 30 \
--genomeDir ../intermediate/Desiree/ \
--readFilesIn \
../input/SRR10416848_1.fastq \
../input/SRR10416848_2.fastq \
--outFileNamePrefix ../output/Desiree_SRR10416848/ \
--outSAMtype BAM SortedByCoordinate

#index bam file
samtools index ../output/Desiree_SRR10416848/Aligned.sortedByCoord.out.bam



# StPGSC4.04n_seq_2_PGSC-t-rep_ITAG-cds_gff-2019-04-23.fasta
# Desiree STAR PE mapping
STAR \
--runMode alignReads \
--runThreadN 30 \
--genomeDir ../intermediate/gff-merged/ \
--readFilesIn \
../input/SRR10416848_1.fastq \
../input/SRR10416848_2.fastq \
--outFileNamePrefix ../output/gff-merged_SRR10416848/ \
--outSAMtype BAM SortedByCoordinate

samtools index ../output/gff-merged_SRR10416848/Aligned.sortedByCoord.out.bam



# PGSC_DM_v3.4_transcript-update_representative.fasta
# Desiree STAR PE mapping
STAR \
--runMode alignReads \
--runThreadN 30 \
--genomeDir ../intermediate/PGSC/ \
--readFilesIn \
../input/SRR10416848_1.fastq \
../input/SRR10416848_2.fastq \
--outFileNamePrefix ../output/PGSC_SRR10416848/ \
--outSAMtype BAM SortedByCoordinate

samtools index ../output/PGSC_SRR10416848/Aligned.sortedByCoord.out.bam




# stCuSTr-D_tr_representatives.fasta
# Desiree STAR PE mapping
STAR \
--runMode alignReads \
--runThreadN 30 \
--genomeDir ../intermediate/Desiree/ \
--readFilesIn \
../input/SRR10416849_1.fastq \
../input/SRR10416849_2.fastq \
--outFileNamePrefix ../output/Desiree_SRR10416849/ \
--outSAMtype BAM SortedByCoordinate

#index bam file
samtools index ../output/Desiree_SRR10416849/Aligned.sortedByCoord.out.bam



# StPGSC4.04n_seq_2_PGSC-t-rep_ITAG-cds_gff-2019-04-23.fasta
# Desiree STAR PE mapping
STAR \
--runMode alignReads \
--runThreadN 30 \
--genomeDir ../intermediate/gff-merged/ \
--readFilesIn \
../input/SRR10416849_1.fastq \
../input/SRR10416849_2.fastq \
--outFileNamePrefix ../output/gff-merged_SRR10416849/ \
--outSAMtype BAM SortedByCoordinate

samtools index ../output/gff-merged_SRR10416849/Aligned.sortedByCoord.out.bam



# PGSC_DM_v3.4_transcript-update_representative.fasta
# Desiree STAR PE mapping
STAR \
--runMode alignReads \
--runThreadN 30 \
--genomeDir ../intermediate/PGSC/ \
--readFilesIn \
../input/SRR10416849_1.fastq \
../input/SRR10416849_2.fastq \
--outFileNamePrefix ../output/PGSC_SRR10416849/ \
--outSAMtype BAM SortedByCoordinate

samtools index ../output/PGSC_SRR10416849/Aligned.sortedByCoord.out.bam


# Multiple samples can be mapped in one job. 
# For single-end reads use a comma separated list (no spaces around commas), e.g. --readFilesIn sample1.fq,sample2.fq,sample3.fq.
# For paired-end reads, use comma separated list for read1 /space/ comma separated list for read2, e.g.: --readFilesIn sample1read1.fq,sample2read1.fq,sample3read1.fq sample1read2.fq,sample2read2.fq,sample3read2.fq.


# stCuSTr-D_tr_representatives.fasta
# Desiree STAR PE mapping
STAR \
--runMode alignReads \
--runThreadN 30 \
--genomeDir ../intermediate/Desiree/ \
--readFilesIn \
../input/SRR10416847_1.fastq,../input/SRR10416848_1.fastq,../input/SRR10416849_1.fastq \
../input/SRR10416847_2.fastq,../input/SRR10416848_2.fastq,../input/SRR10416849_2.fastq \
--outFileNamePrefix ../output/Desiree_drought123/ \
--outSAMtype BAM SortedByCoordinate

#index bam file
samtools index ../output/Desiree_drought123/Aligned.sortedByCoord.out.bam

# StPGSC4.04n_seq_2_PGSC-t-rep_ITAG-cds_gff-2019-04-23.fasta
# Desiree STAR PE mapping
STAR \
--runMode alignReads \
--runThreadN 30 \
--genomeDir ../intermediate/gff-merged/ \
--readFilesIn \
../input/SRR10416847_1.fastq,../input/SRR10416848_1.fastq,../input/SRR10416849_1.fastq \
../input/SRR10416847_2.fastq,../input/SRR10416848_2.fastq,../input/SRR10416849_2.fastq \
--outFileNamePrefix ../output/gff-merged_drought123/ \
--outSAMtype BAM SortedByCoordinate

#index bam file
samtools index ../output/gff-merged_drought123/Aligned.sortedByCoord.out.bam

# PGSC_DM_v3.4_transcript-update_representative.fasta
# Desiree STAR PE mapping
STAR \
--runMode alignReads \
--runThreadN 30 \
--genomeDir ../intermediate/PGSC/ \
--readFilesIn \
../input/SRR10416847_1.fastq,../input/SRR10416848_1.fastq,../input/SRR10416849_1.fastq \
../input/SRR10416847_2.fastq,../input/SRR10416848_2.fastq,../input/SRR10416849_2.fastq \
--outFileNamePrefix ../output/PGSC_drought123/ \
--outSAMtype BAM SortedByCoordinate

#index bam file
samtools index ../output/PGSC_drought123/Aligned.sortedByCoord.out.bam