## Index Lymnaea genome
STAR --runMode genomeGenerate --runThreadN 10 \
--genomeDir ~/genomeDir --genomeFastaFiles ~/LS_genome.fa \
--sjdbGTFfile ~LS.gtf --sjdbOverhang 100
## Map raw reads to reference genome
STAR --genomeDir ~/genomeDir --runThreadN 6 \
--readFilesIn BYD_AEOSRB_7_1_HJLK5BBXX.12BA015_noribo_clean.fastq BYD_AEOSRB_7_2_HJLK5BBXX.12BA015_noribo_clean.fastq \
--outFileNamePrefix AE_raw --seedPerReadNmax 10000 --sjdbGTFfile ~/LS.gtf --sjdbOverhang 100 \
--twopassMode Basic --outReadsUnmapped Fastx --outSAMtype BAM SortedByCoordinate
## Infer strand orientation
infer_experiment.py -i AE_rawAligned.sortedByCoord.out.bam -r ~/LS.bed -s 1000000
Orientation: Fr-first strand (RF)
## Map raw reads to reference genome
STAR --genomeDir ~/genomeDir --runThreadN 6 \
--readFilesIn BYD_AFOSRB_7_1_HJLK5BBXX.12BA016_noribo_clean.fastq BYD_AFOSRB_7_2_HJLK5BBXX.12BA016_noribo_clean.fastq \
--outFileNamePrefix AF_raw --seedPerReadNmax 10000 --sjdbGTFfile ~/LS.gtf --sjdbOverhang 100 \
--twopassMode Basic --outReadsUnmapped Fastx --outSAMtype BAM SortedByCoordinate
## Infer strand orientation
infer_experiment.py -i AF_rawAligned.sortedByCoord.out.bam -r ~/LS.bed -s 1000000
Orientation: Fr-first strand (RF)
## Map raw reads to reference genome
STAR --genomeDir ~/genomeDir --runThreadN 8 \
--readFilesIn BYD_AGOSRB_7_1_HJLK5BBXX.12BA017_noribo_clean.fastq BYD_AGOSRB_7_2_HJLK5BBXX.12BA017_noribo_clean.fastq \
--outFileNamePrefix AG_raw --seedPerReadNmax 10000 --sjdbGTFfile ~/LS.gtf --sjdbOverhang 100 \
--twopassMode Basic --outReadsUnmapped Fastx --outSAMtype BAM SortedByCoordinate
## Infer strand orientation
infer_experiment.py -i AG_rawAligned.sortedByCoord.out.bam -r ~/LS.bed -s 1000000
Orientation: Fr-first strand (RF)
## Map raw reads to reference genome
STAR --genomeDir ~/genomeDir --runThreadN 8 \
--readFilesIn BYD_AHOSRB_7_1_HJLK5BBXX.12BA018_noribo_clean.fastq BYD_AHOSRB_7_2_HJLK5BBXX.12BA018_noribo_clean.fastq \
--outFileNamePrefix AH_raw --seedPerReadNmax 10000 --sjdbGTFfile ~/LS.gtf --sjdbOverhang 100 \
--twopassMode Basic --outReadsUnmapped Fastx --outSAMtype BAM SortedByCoordinate
## Infer strand orientation
infer_experiment.py -i AH_rawAligned.sortedByCoord.out.bam -r ~/LS.bed -s 1000000
Orientation: Fr-first strand (RF)
## Map raw reads to reference genome
STAR --genomeDir ~/genomeDir --runThreadN 8 \
--readFilesIn DRR002012_1.fastq \
--outFileNamePrefix DRR_raw --seedPerReadNmax 10000 --sjdbGTFfile ~/LS.gtf --sjdbOverhang 100 \
--twopassMode Basic --outReadsUnmapped Fastx --outSAMtype BAM SortedByCoordinate
## Infer strand orientation
infer_experiment.py -i DRR_corrected_Dec3Aligned.sortedByCoord.out.bam -r ~/LS.bed -s 1000000
Orientation: Unstranded
## AE
fastqc -o . --noextract -f fastq ./BYD_AEOSRB_7_1_HJLK5BBXX.12BA015_noribo_clean.fastq -t 8
fastqc -o . --noextract -f fastq ./BYD_AEOSRB_7_2_HJLK5BBXX.12BA015_noribo_clean.fastq -t 8
## AF
fastqc -o . --noextract -f fastq ./BYD_AFOSRB_7_1_HJLK5BBXX.12BA016_noribo_clean.fastq -t 8
fastqc -o . --noextract -f fastq ./BYD_AFOSRB_7_2_HJLK5BBXX.12BA016_noribo_clean.fastq -t 8
## AG
fastqc -o . --noextract -f fastq ./BYD_AGOSRB_7_1_HJLK5BBXX.12BA017_noribo_clean.fastq -t 8
fastqc -o . --noextract -f fastq ./BYD_AGOSRB_7_2_HJLK5BBXX.12BA017_noribo_clean.fastq -t 8
## AH
fastqc -o . --noextract -f fastq ./BYD_AHOSRB_7_1_HJLK5BBXX.12BA018_noribo_clean.fastq -t 8
fastqc -o . --noextract -f fastq ./BYD_AHOSRB_7_2_HJLK5BBXX.12BA018_noribo_clean.fastq -t 8
## DRR
fastqc -o . --noextract -f fastq ./DRR002012_1.fastq -t 8
## rCorrector
perl ~/install/Rcorrector-master/run_rcorrector.pl -t 10 \
-1 ./BYD_AEOSRB_7_1_HJLK5BBXX.12BA015_noribo_clean.fastq \
-2 ./BYD_AEOSRB_7_2_HJLK5BBXX.12BA015_noribo_clean.fastq
## Remove unfixable reads
python ~/FilterUncorrectabledPEfastq.py \
-1 RNA-Seq_reads/BYD_AEOSRB_7_1_HJLK5BBXX.12BA015_noribo_clean.cor.fq \
-2 RNA-Seq_reads/BYD_AEOSRB_7_2_HJLK5BBXX.12BA015_noribo_clean.cor.fq \
-o AE_corrected
## FastQC
fastqc -o . --noextract -f fastq ./AE_corrected_BYD_AEOSRB_7_1_HJLK5BBXX.12BA015_noribo_clean.cor.fq -t 8
fastqc -o . --noextract -f fastq ./AE_corrected_BYD_AEOSRB_7_2_HJLK5BBXX.12BA015_noribo_clean.cor.fq -t 8
## rCorrector
perl ~/install/Rcorrector-master/run_rcorrector.pl -t 10 \
-1 ./BYD_AFOSRB_7_1_HJLK5BBXX.12BA016_noribo_clean.fastq \
-2 ./BYD_AFOSRB_7_2_HJLK5BBXX.12BA016_noribo_clean.fastq
## Remove unfixable reads
python ~/FilterUncorrectabledPEfastq.py \
-1 RNA-Seq_reads/BYD_AFOSRB_7_1_HJLK5BBXX.12BA016_noribo_clean.cor.fq \
-2 RNA-Seq_reads/BYD_AFOSRB_7_2_HJLK5BBXX.12BA016_noribo_clean.cor.fq \
-o AF_corrected
## FastQC
fastqc -o . --noextract -f fastq ./AF_corrected_BYD_AFOSRB_7_1_HJLK5BBXX.12BA016_noribo_clean.cor.fq -t 8
fastqc -o . --noextract -f fastq ./AF_corrected_BYD_AFOSRB_7_2_HJLK5BBXX.12BA016_noribo_clean.cor.fq -t 8
## rCorrector [25483945.bc]
perl ~/install/Rcorrector-master/run_rcorrector.pl -t 10 \
-1 ./BYD_AGOSRB_7_1_HJLK5BBXX.12BA017_noribo_clean.fastq \
-2 ./BYD_AGOSRB_7_2_HJLK5BBXX.12BA017_noribo_clean.fastq
## Remove unfixable reads [25483952.bc]
python ~/FilterUncorrectabledPEfastq.py \
-1 RNA-Seq_reads/BYD_AGOSRB_7_1_HJLK5BBXX.12BA017_noribo_clean.cor.fq \
-2 RNA-Seq_reads/BYD_AGOSRB_7_2_HJLK5BBXX.12BA017_noribo_clean.cor.fq \
-o AG_corrected
## FastQC
fastqc -o . --noextract -f fastq ./AG_corrected_BYD_AGOSRB_7_1_HJLK5BBXX.12BA017_noribo_clean.cor.fq -t 8
fastqc -o . --noextract -f fastq ./AG_corrected_BYD_AGOSRB_7_2_HJLK5BBXX.12BA017_noribo_clean.cor.fq -t 8
## rCorrector
perl ~/install/Rcorrector-master/run_rcorrector.pl -t 10 \
-1 ./BYD_AHOSRB_7_1_HJLK5BBXX.12BA018_noribo_clean.fastq \
-2 ./BYD_AHOSRB_7_2_HJLK5BBXX.12BA018_noribo_clean.fastq
## Remove unfixable reads
python ~/FilterUncorrectabledPEfastq.py \
-1 RNA-Seq_reads/BYD_AHOSRB_7_1_HJLK5BBXX.12BA018_noribo_clean.cor.fq \
-2 RNA-Seq_reads/BYD_AHOSRB_7_2_HJLK5BBXX.12BA018_noribo_clean.cor.fq \
-o AH_corrected
## FastQC
fastqc -o . --noextract -f fastq ./AH_corrected_BYD_AHOSRB_7_1_HJLK5BBXX.12BA018_noribo_clean.cor.fq -t 8
fastqc -o . --noextract -f fastq ./AH_corrected_BYD_AHOSRB_7_2_HJLK5BBXX.12BA018_noribo_clean.cor.fq -t 8
## rCorrector
perl ~/install/Rcorrector-master/run_rcorrector.pl -t 10 -s ./DRR002012_1.fastq
## Remove unfixable reads
python ~/FilterUncorrectabledSEfastq.py -i DRR002012_1.cor.fq -o filtered_
## FastQC
fastqc -o . --noextract -f fastq ./filtered_DRR002012_1.cor.fq -t 8
Output: LS_multiqc_report.html
multiqc .