Transcript assembly commands

1 Set the genome environment variable

export genome=Inputs/Reference/Athaliana_447_TAIR10_Chr3_clean.fa

2 Build Hisat2 index

rm -rf Hisat2 Stringtie Scallop Assemblies && mkdir -p Hisat2/db && hisat2-build $genome Hisat2/db/$(basename $genome .fa) > Hisat2/index.log 2>&1

3 Perform HISAT2 alignment for each set of reads

for folder in Inputs/Reads/SR*; do echo -e "\n\n## Running Hisat2 on sample ${folder} ..." && folder=$(basename $folder) && mkdir -p Hisat2/${folder} && hisat2 --max-intronlen 50000  --rna-strandness RF -p 2 -x Hisat2/db/Athaliana_447_TAIR10_Chr3_clean -1 Inputs/Reads/${folder}/*R1.*fastq.gz -2 Inputs/Reads/${folder}/*R2.*fastq.gz | samtools sort -@ 2 -o Hisat2/${folder}/Hisat2.bam; done

4 Transcript assemblies

mkdir -p Assemblies

4.1 Stringtie

for folder in Inputs/Reads/SRR*; do echo -ne "\n\n## Running stringtie on sample ${folder} ..." && folder=$(basename ${folder}) && mkdir -p Assemblies && mkdir -p Stringtie/${folder} && stringtie Hisat2/${folder}/Hisat2.bam -o Stringtie/${folder}/${folder}.gtf > Stringtie/${folder}/stringtie.log 2>&1 && cp Stringtie/${folder}/${folder}.gtf Assemblies/stringtie-${folder}.gtf && echo done; done

4.2 Scallop

for folder in Inputs/Reads/SRR*; do echo -ne "\n\n## Running scallop on sample ${folder} ..." && folder=$(basename ${folder}) && mkdir -p Assemblies && mkdir -p Scallop/${folder} && scallop -i Hisat2/${folder}/Hisat2.bam -o Scallop/${folder}/${folder}.gtf > Scallop/${folder}/scallop.log 2>&1 && cp Scallop/${folder}/${folder}.gtf Assemblies/scallop-${folder}.gtf && echo done;done

5 Portcullis

for folder in Inputs/Reads/SRR*; do echo -ne "\n\n## Running portcullis on sample ${folder} ..." && cd Hisat2/$(basename ${folder}) && rm -rf portcullis && portcullis prep -o portcullis/1-prep ../../$genome Hisat2.bam > prep.log 2>&1 && portcullis junc -o portcullis/2-junc/portcullis portcullis/1-prep > junc.log 2>&1 && portcullis filt -o portcullis/3-filt/portcullis portcullis/1-prep portcullis/2-junc/portcullis*tab > filt.log 2>&1 && cd ../.. && echo done;done