adjusted paths to ARC structure

assays/BSA_RNAseq/adapters/custom_adapters.fa

+>read1_1/1
+AGATCGGAAGAGCACACGTCTGAACTCCAGTCA
+>read1_2/1
+AGATCGGAAGAGCACACGTCTGAAC
+>read1_3/1
+TGGAATTCTCGGGTGCCAAGG
+>read1_4/1
+AGATCGGAAGAGCACACGTCT
+>read1_5/1
+CTGTCTCTTATACACATCT
+>read1_6/1
+AGATGTGTATAAGAGACAG
+>read2_1/2
+AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGT
+>read2_2/2
+AGATCGGAAGAGCGTCGTGTAGGGA
+>read2_3/2
+TGGAATTCTCGGGTGCCAAGG
+>read2_4/2
+AGATCGGAAGAGCACACGTCT
+>read2_5/2
+CTGTCTCTTATACACATCT
+>read2_6/2
+AGATGTGTATAAGAGACAG

assays/BSA_RNAseq/adapters/readme.txt

+## raw_data/BSA_rnaseq/adapters/
+
+Sequencing adapters used for reads trimming

studies/additional_data/resources/color_pathway_genes.bed

+chr	start	end	strand	gene_id	transcript_id	Gene	Pathway
+Scaffold_1	7523181	7527088	-	AHp000674	AHp000674.1	AhCYP76AD5	Betalain
+Scaffold_1	28687404	28688868	-	AHp001663	AHp001663.1	AhBetanidin5GT	Betalain
+Scaffold_2	6806355	6807984	+	AHp003152	AHp003152.1	F3-H_3	Flavonoid
+Scaffold_2	6806355	6807984	+	AHp003152	AHp003152.2	F3-H_3	Flavonoid
+Scaffold_2	31518210	31522095	+	AHp004305	AHp004305.1	CHS	Flavonoid
+Scaffold_2	31518210	31522095	+	AHp004305	AHp004305.2	CHS	Flavonoid
+Scaffold_3	14652200	14653652	+	AHp005940	AHp005940.1	AhBetanidin6GT	Betalain
+Scaffold_3	29507485	29509926	+	AHp006454	AHp006454.1	F3H	Flavonoid
+Scaffold_4	10226509	10227946	-	AHp007219	AHp007219.1	AhcDOPA5GT	Betalain
+Scaffold_5	9470955	9474986	-	AHp008991	AHp008991.1	FLS	Flavonoid
+Scaffold_5	9470955	9474986	-	AHp008991	AHp008991.2	FLS	Flavonoid
+Scaffold_5	19537497	19543306	+	AHp009303	AHp009303.1	DFR	Flavonoid
+Scaffold_6	3461614	3469253	-	AHp009962	AHp009962.1	CHI1	Flavonoid
+Scaffold_6	13877397	13882497	+	AHp010386	AHp010386.1	AhDODAα2	Betalain
+Scaffold_8	3308349	3313908	+	AHp012752	AHp012752.1	PAL_1	Flavonoid
+Scaffold_8	7925628	7930892	-	AHp013217	AHp013217.1	C4H_1	Flavonoid
+Scaffold_8	7925628	7930892	-	AHp013217	AHp013217.2	C4H_1	Flavonoid
+Scaffold_9	12115220	12125730	-	AHp014409	AHp014409.1	4CL_1	Flavonoid
+Scaffold_10	21762620	21764924	-	AHp016530	AHp016530.1	AhMYB3	Betalain
+Scaffold_10	21780564	21783050	-	AHp016531	AHp016531.1	AhMYB4	Betalain
+Scaffold_11	16155424	16159543	+	AHp017409	AHp017409.1	LAR	Flavonoid
+Scaffold_11	17204504	17209738	-	AHp017497	AHp017497.1	F3-H_1	Flavonoid
+Scaffold_14	12286837	12295353	+	AHp020962	AHp020962.1	4CL_2	Flavonoid
+Scaffold_15	1098208	1100359	+	AHp021795	AHp021795.1	ANS	Flavonoid
+Scaffold_15	2886482	2891165	-	AHp021980	AHp021980.1	PAL_2	Flavonoid
+Scaffold_15	4193988	4197809	+	AHp022120	AHp022120.1	F3-H_4	Flavonoid
+Scaffold_15	4211064	4214362	+	AHp022122	AHp022122.1	F3-H_2	Flavonoid
+Scaffold_15	4227367	4229108	-	AHp022123	AHp022123.1	F3-H_5	Flavonoid
+Scaffold_15	7959672	7965298	+	AHp022382	AHp022382.1	C4H_3	Flavonoid
+Scaffold_15	7959672	7965298	+	AHp022382	AHp022382.2	C4H_3	Flavonoid
+Scaffold_15	8003999	8008333	+	AHp022384	AHp022384.1	C4H_2	Flavonoid
+Scaffold_16	988733	991447	+	AHp022773	AHp022773.1	AhMYB2	Betalain
+Scaffold_16	988733	991447	+	AHp022773	AHp022773.2	AhMYB2	Betalain
+Scaffold_16	5231548	5239058	-	AHp023147	AHp023147.1	AhDODAα1	Betalain
+Scaffold_16	5301961	5305973	+	AHp023148	AHp023148.1	AhCYP76AD2	Betalain

studies/additional_data/resources/color_pathway_genes.csv

+Gene,Pathway,Gene_id
+PAL_1,Flavonoid,AHp012752
+PAL_2,Flavonoid,AHp021980
+C4H_1,Flavonoid,AHp013217
+C4H_2,Flavonoid,AHp022384
+C4H_3,Flavonoid,AHp022382
+4CL_1,Flavonoid,AHp014409
+4CL_2,Flavonoid,AHp020962
+CHS,Flavonoid,AHp004305
+CHI1,Flavonoid,AHp009962
+F3-H_1,Flavonoid,AHp017497
+F3-H_2,Flavonoid,AHp022122
+F3-H_3,Flavonoid,AHp003152
+F3-H_4,Flavonoid,AHp022120
+F3-H_5,Flavonoid,AHp022123
+DFR,Flavonoid,AHp009303
+F3H,Flavonoid,AHp006454
+FLS,Flavonoid,AHp008991
+LAR,Flavonoid,AHp017409
+ANS,Flavonoid,AHp021795
+AhCYP76AD2,Betalain,AHp023148
+AhCYP76AD5,Betalain,AHp000674
+AhDODAα2,Betalain,AHp010386
+AhDODAα1,Betalain,AHp023147
+AhcDOPA5GT,Betalain,AHp007219
+AhBetanidin5GT,Betalain,AHp001663
+AhBetanidin6GT,Betalain,AHp005940
+AhMYB2,Betalain,AHp022773
+AhMYB3,Betalain,AHp016530
+AhMYB4,Betalain,AHp016531

workflows/BSA/RNAseq/QC.sh

@@ -22,8 +22,8 @@ GTFIN=polished_genome_annotation/annotation/Ahypochondriacus_2.2_polished_correc
 
 # Quality control
 # Initialize the output directory
-QCIN=raw_data/BSA_rnaseq/
-QCOUT=raw_data/BSA_rnaseq/fastqc
+QCIN=assays/BSA_RNAseq/dataset
+QCOUT=assays/BSA_RNAseq/fastqc
 
 mkdir -p $QCOUT
 # run quality control fastqc
@@ -32,14 +32,14 @@ fastqc -t 10 -o $QCOUT "$QCIN"*P.fq.gz
 
 # Quality control
 # Initialize the output directory
-QCIN=raw_data/BSA_rnaseq/
-QCOUT=raw_data/BSA_rnaseq/fastqc
+QCIN=assays/BSA_RNAseq/
+QCOUT=assays/BSA_RNAseq/fastqc
 
 mkdir -p $QCOUT
 # run quality control fastqc
 fastqc -t 10 -o $QCOUT "$QCIN"*P.fq.gz
 
-cp -r $QCOUT data/BSA/RNAseq/STAR_flower_mappings/QC/
+cp -r $QCOUT runs/BSA/RNAseq/STAR_flower_mappings/QC/
 
 module load samtools/1.13
 
@@ -53,11 +53,11 @@ GTFQM=/scratch/twinkle1/temp.gtf
 sed 's/CDS/exon/' $GTFIN > $GTFQM
 
 # define input files
-QMIN=data/BSA/RNAseq/STAR_flower_mappings/
+QMIN=runs/BSA/RNAseq/STAR_flower_mappings/
 
 
 # define output directory
-QMOUT=data/BSA/RNAseq/STAR_flower_mappings/QC/qualimap
+QMOUT=runs/BSA/RNAseq/STAR_flower_mappings/QC/qualimap
 
 # create main output directory
 mkdir -p $QMOUT
@@ -85,8 +85,8 @@ done
 rm $GTFQM
 
 # run multiqc to combine the results from fastqc and qualimap into a single report
-MULTIQCOUT=data/BSA/RNAseq/STAR_flower_mappings/multiqc
-MULTIQCIN=data/BSA/RNAseq/STAR_flower_mappings/QC/
+MULTIQCOUT=runs/BSA/RNAseq/STAR_flower_mappings/multiqc
+MULTIQCIN=runs/BSA/RNAseq/STAR_flower_mappings/QC/
 
 mkdir -p $MULTIQCOUT
 

workflows/BSA/RNAseq/adapter_trimming.sh

@@ -20,7 +20,7 @@ module load trimmomatic/0.39
 
 # run this part as array job
 # create array of read fastq files (R1 only):
-SOURCE_DIR=raw_data/BSA_rnaseq/
+SOURCE_DIR=assays/BSA_RNAseq/dataset/
 FILES=("$SOURCE_DIR"/*R1.fastq.gz)
 
 # run trimmomatic, use 6 threads, taking advantage of the baseout function to name output files
@@ -32,4 +32,4 @@ java -jar $TRIMMOMATIC/trimmomatic.jar PE \
 	"${FILES["${SLURM_ARRAY_TASK_ID}"]}" \
 	"${FILES["${SLURM_ARRAY_TASK_ID}"]/R1.fastq.gz/R2.fastq.gz}" \
 	-baseout "${FILES["${SLURM_ARRAY_TASK_ID}"]/R1.fastq.gz/trimmed.fq.gz}" \
-	ILLUMINACLIP:raw_data/BSA_rnaseq/adapters/custom_adapters.fa:2:30:10
+	ILLUMINACLIP:assays/BSA_RNAseq/adapters/custom_adapters.fa:2:30:10

workflows/BSA/RNAseq/index_STAR.sh

@@ -18,10 +18,10 @@ module load star/2.7.8a
 # more specific settings: use the polished, softmasked reference assembly
 # sjdbOverhang dependend on input read length
 # as SJDB file, use the newly generated braker2 protein gtf file
-REFGENOME=polished_genome_annotation/assembly/Ahypochondriacus_2.2_polished.softmasked.fasta
-SJDBFILE=polished_genome_annotation/annotation/Ahypochondriacus_2.2_polished_corrected.gtf
+REFGENOME=runs/polished_genome_annotation/assembly/Ahypochondriacus_2.2_polished.softmasked.fasta
+SJDBFILE=runs/polished_genome_annotation/annotation/Ahypochondriacus_2.2_polished_corrected.gtf
 
-mkdir -p data/BSA/RNAseq/STAR_flower_index
+mkdir -p runs/BSA/RNAseq/STAR_flower_index
 
 STAR --runThreadN 8 \
 	--runMode genomeGenerate \