## Assembly
stringtie ~/AE_corrected_filtered_Nov14_GTF_refAligned.sortedByCoord.out.bam \
-l Nov14_AE_gtf -o Nov14_AE_gtf.gff -p 8 -v --rf -A Nov14_AE_gtf.tab
## Extract transcripts
gffread ~/Nov14_AE_gtf.gff -g ~/database/Genomes/LS/LS_genome.fa -w ~/stringtie_Nov14_AE_gtf.fa
## Assembly
stringtie ~/AF_corrected_filtered_Nov14_GTF_refAligned.sortedByCoord.out.bam \
-l Nov14_AF_gtf -o Nov14_AF_gtf.gff -p 8 -v --rf -A Nov14_AF_gtf.tab
## Extract transcripts
gffread ~/Nov14_AF_gtf.gff -g ~/database/Genomes/LS/LS_genome.fa -w ~/stringtie_Nov14_AF_gtf.fa
## Assembly
stringtie ~/AG_corrected_filtered_Nov14_GTF_refAligned.sortedByCoord.out.bam \
-l Nov14_AG_gtf -o Nov14_AG_gtf.gff -p 8 -v --rf -A Nov14_AG_gtf.tab
## Extract transcripts
gffread ~/Nov14_AG_gtf.gff -g ~/database/Genomes/LS/LS_genome.fa -w ~/stringtie_Nov14_AG_gtf.fa
## Assembly
stringtie ~/AH_corrected_filtered_Nov14_GTF_refAligned.sortedByCoord.out.bam \
-l Nov14_AH_gtf -o Nov14_AH_gtf.gff -p 8 -v --rf -A Nov14_AH_gtf.tab
## Extract transcripts
gffread ~/Nov14_AH_gtf.gff -g ~/database/Genomes/LS/LS_genome.fa -w ~/stringtie_Nov14_AH_gtf.fa
## Assembly [27049165.bc]
scallop -i ~/AE_corrected_filtered_Nov14_GTF_refAligned.sortedByCoord.out.bam \
-o scallop_Dec30_AE_gtf.gff --library_type first --verbose 0
## Extract transcripts
gffread ~/scallop_Dec30_AE_gtf.gff -g ~/database/Genomes/LS/LS_genome.fa -w ~/scallop_Dec30_AE_gtf.fa
## Assembly [27049166.bc]
scallop -i ~/AF_corrected_filtered_Nov14_GTF_refAligned.sortedByCoord.out.bam \
-o scallop_Dec30_AF_gtf.gff --library_type first --verbose 0
## Extract transcripts
gffread ~/scallop_Dec30_AF_gtf.gff -g ~/database/Genomes/LS/LS_genome.fa -w ~/scallop_Dec30_AF_gtf.fa
## Assembly [27049164.bc]
scallop -i ~/AG_corrected_filtered_Nov14_GTF_refAligned.sortedByCoord.out.bam \
-o scallop_Dec30_AG_gtf.gff --library_type first --verbose 0
## Extract transcripts
gffread ~/scallop_Dec30_AG_gtf.gff -g ~/database/Genomes/LS/LS_genome.fa -w ~/scallop_Dec30_AG_gtf.fa
## Assembly [27049167.bc]
scallop -i ~/AH_corrected_filtered_Nov14_GTF_refAligned.sortedByCoord.out.bam \
-o scallop_Dec30_AH_gtf.gff --library_type first --verbose 0
## Extract transcripts
gffread ~/scallop_Dec30_AH_gtf.gff -g ~/database/Genomes/LS/LS_genome.fa -w ~/scallop_Dec30_AH_gtf.fa
## Assembly [27049052.bc]
strawberry -o ~/strawberry_AE_Dec30 --no-quant -p 10 -v ~/AE_corrected_filtered_Nov14_GTF_refAligned.sortedByCoord.out.bam
## Extract transcripts
gffread ~/strawberry_AE_Dec30/strawberry_AE_Dec30_assembled_transcripts.gtf -g ~/database/Genomes/LS/LS_genome.fa \
-w ~/strawberry_AE_Dec30_assembled_transcripts.fa
## Assembly [27049054.bc]
strawberry -o ~/strawberry_AF_Dec30 --no-quant -p 10 -v \
~/AF_corrected_filtered_Nov14_GTF_refAligned.sortedByCoord.out.bam
## Extract transcripts
gffread ~/strawberry_AF_Dec30/strawberry_AF_Dec30_assembled_transcripts.gtf -g ~/database/Genomes/LS/LS_genome.fa \
-w ~/strawberry_AF_Dec30_assembled_transcripts.fa
## Assembly [27049055.bc]
strawberry -o ~/strawberry_AG_Dec30 --no-quant -p 10 -v \
~/AG_corrected_filtered_Nov14_GTF_refAligned.sortedByCoord.out.bam
## Extract transcripts
gffread ~/strawberry_AG_Dec30/strawberry_AG_Dec30_assembled_transcripts.gtf -g ~/database/Genomes/LS/LS_genome.fa \
-w ~/strawberry_AG_Dec30_assembled_transcripts.fa
## Assembly [27049053.bc]
strawberry -o ~/strawberry_AH_Dec30 --no-quant -p 10 -v \
~/AH_corrected_filtered_Nov14_GTF_refAligned.sortedByCoord.out.bam
## Extract transcripts
gffread ~/strawberry_AH_Dec30/strawberry_AH_Dec30_assembled_transcripts.gtf -g ~/database/Genomes/LS/LS_genome.fa \
-w ~/strawberry_AH_Dec30_assembled_transcripts.fa
## [27049168.bc]
Trinity --genome_guided_bam ~/AE_corrected_filtered_Nov14_GTF_refAligned.sortedByCoord.out.bam --max_memory 30G \
--CPU 10 --verbose --output ~/Trinity_AE_genome_guided_Dec30 --SS_lib_type RF \
--genome_guided_max_intron 10000 --no_bowtie
## [27049169.bc]
Trinity --genome_guided_bam ~/AF_corrected_filtered_Nov14_GTF_refAligned.sortedByCoord.out.bam --max_memory 30G \
--CPU 10 --verbose --output ~/Trinity_AF_genome_guided_Dec30 --SS_lib_type RF \
--genome_guided_max_intron 10000 --no_bowtie
## [27049372.bc]
Trinity --genome_guided_bam ~/AG_corrected_filtered_Nov14_GTF_refAligned.sortedByCoord.out.bam --max_memory 30G \
--CPU 10 --verbose --output ~/Trinity_AG_genome_guided_Dec30 --SS_lib_type RF \
--genome_guided_max_intron 10000 --no_bowtie
## [27049373.bc]
Trinity --genome_guided_bam ~/AH_corrected_filtered_Nov14_GTF_refAligned.sortedByCoord.out.bam --max_memory 30G \
--CPU 10 --verbose --output ~/Trinity_AH_genome_guided_Dec30 --SS_lib_type RF \
--genome_guided_max_intron 10000 --no_bowtie
## [26594651.bc]
Trinity --seqType fq --max_memory 100G \
--left \
AE_corrected_filtered_Nov14_GTF_refUnmapped_1.fq, \
AF_corrected_filtered_Nov14_GTF_refUnmapped_1.fq, \
AG_corrected_filtered_Nov14_GTF_refUnmapped_1.fq, \
AH_corrected_filtered_Nov14_GTF_refUnmapped_1.fq \
--right \
AE_corrected_filtered_Nov14_GTF_refUnmapped_2.fq, \
AF_corrected_filtered_Nov14_GTF_refUnmapped_2.fq, \
AG_corrected_filtered_Nov14_GTF_refUnmapped_2.fq, \
AH_corrected_filtered_Nov14_GTF_refUnmapped_2.fq \
--CPU 15 --SS_lib_type RF --verbose \
--output ~/Trinity_RF_Nov18 --no_bowtie
## Assembly [27691864.bc]
stringtie DRR_filtered_corrected_Mar28Aligned.sortedByCoord.out.bam \
-l Mar28_DRR -o Mar28_DRR_noref.gff -p 10 -v
## Extract transcripts
gffread Mar28_DRR_noref.gff -g database/Genomes/LS/LS_genome.fa -E -w ~/Mar28_DRR_ST_transcripts.fa
## Assembly [27691869.bc]
scallop -i DRR_filtered_corrected_Mar28Aligned.sortedByCoord.out.bam -o DRR_scallop_Mar28.gff \
--library_type unstranded --verbose 0
## Extract transcripts
gffread DRR_scallop_Mar28.gff -g database/Genomes/LS/LS_genome.fa -E -w ~/Mar28_DRR_scallop_transcripts.fa
## Assembly [27691921.bc]
strawberry -o ~/Strawberry_DRR_Mar28 --no-quant -p 15 -v ~/DRR_filtered_corrected_Mar28Aligned.sortedByCoord.out.bam
## Extract transcripts
gffread ~/Strawberry_DRR_Mar28/assembled_transcripts.gtf -g database/Genomes/LS/LS_genome.fa \
-E -w ~/LS_strawberry_DRR_transcripts_Mar28.fa
## [27691924.bc]
Trinity --genome_guided_bam ~/DRR_filtered_corrected_Mar28Aligned.sortedByCoord.out.bam \
--max_memory 20G --genome_guided_max_intron 10000 --CPU 10 --verbose --output ~/Trinity_GG_LS_DRR_Mar28 --no_bowtie
# Reads need to have "/1" at the end of ID for Trinity to recognize it
sed '1~4 s/$/\/1/g' DRR_filtered_corrected_Mar28Unmapped.fq > DRR_filtered_corrected_Mar28Unmapped_renamed.fq
# De novo assembly [27697292.bc]
Trinity --seqType fq --max_memory 100G \
--single ~/DRR_filtered_corrected_Mar28Unmapped_renamed.fq --CPU 8 --verbose \
--output ~/Trinity_DRR_unmapped_Mar30_renamed --no_bowtie