gffread ./LS_GFF.gff -T -o LS_GTF.gtf
STAR --runThreadN 8 \
--runMode genomeGenerate \
--genomeDir ~/LS_genome_index_Nov14_GTF \
--genomeFastaFiles database/Genomes/LS/LS_genome.fa \
--sjdbGTFfile database/Genomes/LS/LS_GTF.gtf \
--sjdbOverhang 149
STAR --genomeDir ~/LS_genome_index_Nov14_GTF \
--runThreadN 8 \
--readFilesIn \
RNA-Seq_reads/AE_corrected_BYD_AEOSRB_7_1_HJLK5BBXX.12BA015_noribo_clean.cor.fq \
RNA-Seq_reads/AE_corrected_BYD_AEOSRB_7_2_HJLK5BBXX.12BA015_noribo_clean.cor.fq \
--outFileNamePrefix AE_corrected_filtered_Nov14_GTF_ref \
--seedPerReadNmax 10000 --sjdbGTFfile database/Genomes/LS/LS_GTF.gtf \
--sjdbOverhang 150 --twopassMode Basic --outReadsUnmapped Fastx --outSAMtype BAM SortedByCoordinate \
--outSAMstrandField intronMotif \
--outSAMattributes NH HI AS nM NM MD jM jI XS ch \
--outSAMattrIHstart 0
> STAR --genomeDir ~/LS_genome_index_Nov14_GTF \
--runThreadN 8 \
--readFilesIn \
RNA-Seq_reads/AF_corrected_BYD_AFOSRB_7_1_HJLK5BBXX.12BA016_noribo_clean.cor.fq \
RNA-Seq_reads/AF_corrected_BYD_AFOSRB_7_2_HJLK5BBXX.12BA016_noribo_clean.cor.fq \
--outFileNamePrefix AF_corrected_filtered_Nov14_GTF_ref --seedPerReadNmax 10000 \
--sjdbGTFfile database/Genomes/LS/LS_GTF.gtf --sjdbOverhang 150 --twopassMode Basic \
--outReadsUnmapped Fastx --outSAMtype BAM SortedByCoordinate \
--outSAMstrandField intronMotif \
--outSAMattributes NH HI AS nM NM MD jM jI XS ch \
--outSAMattrIHstart 0
> STAR --genomeDir ~/LS_genome_index_Nov14_GTF \
--runThreadN 8 \
--readFilesIn \
RNA-Seq_reads/AG_corrected_BYD_AGOSRB_7_1_HJLK5BBXX.12BA017_noribo_clean.cor.fq \
RNA-Seq_reads/AG_corrected_BYD_AGOSRB_7_2_HJLK5BBXX.12BA017_noribo_clean.cor.fq \
--outFileNamePrefix AG_corrected_filtered_Nov14_GTF_ref --seedPerReadNmax 10000 \
--sjdbGTFfile database/Genomes/LS/LS_GTF.gtf --sjdbOverhang 150 --twopassMode Basic \
--outReadsUnmapped Fastx --outSAMtype BAM SortedByCoordinate --outSAMstrandField intronMotif \
--outSAMattributes NH HI AS nM NM MD jM jI XS ch \
--outSAMattrIHstart 0
> STAR --genomeDir ~/LS_genome_index_Nov14_GTF \
--runThreadN 8 \
--readFilesIn \
RNA-Seq_reads/AH_corrected_BYD_AHOSRB_7_1_HJLK5BBXX.12BA018_noribo_clean.cor.fq \
RNA-Seq_reads/AH_corrected_BYD_AHOSRB_7_2_HJLK5BBXX.12BA018_noribo_clean.cor.fq \
--outFileNamePrefix AH_corrected_filtered_Nov14_GTF_ref --seedPerReadNmax 10000 \
--sjdbGTFfile database/Genomes/LS/LS_GTF.gtf --sjdbOverhang 150 --twopassMode Basic \
--outReadsUnmapped Fastx --outSAMtype BAM SortedByCoordinate --outSAMstrandField intronMotif\
--outSAMattributes NH HI AS nM NM MD jM jI XS ch \
--outSAMattrIHstart 0
> STAR --runMode genomeGenerate --runThreadN 15 \
--genomeDir /home/zhanglab1/ndong/LS_genome_index_Dec3_GTF_for_DRR \
--genomeFastaFiles database/Genomes/LS/LS_genome.fa \
--sjdbGTFfile database/Genomes/LS/LS_GTF.gtf --sjdbOverhang 99
[27691630.bc]
> STAR --genomeDir ~/LS_genome_index_Dec3_GTF_for_DRR \
--runThreadN 10 \
--readFilesIn RNA-Seq_reads/filtered_DRR002012_1.cor.fq \
--outFileNamePrefix DRR_filtered_corrected_Mar28 --seedPerReadNmax 10000 \
--sjdbGTFfile ~/database/Genomes/LS/LS_GTF.gtf \
--sjdbOverhang 99 --twopassMode Basic --outReadsUnmapped Fastx \
--outSAMtype BAM SortedByCoordinate --outSAMstrandField intronMotif \
--outSAMattributes NH HI AS nM NM MD jM jI XS ch --outSAMattrIHstart 0
multiqc .