RNA-seq Bioinformatics

Introduction to bioinformatics for RNA sequence analysis

De Novo Transcript Assembly


Running Stringtie in De Novo Mode

Note, to discover novel transcripts with Stringtie using the alignments we generated in the previous modules we will now run Stringtie in de novo mode. To use de novo mode do NOT specify either of the -G OR -e options.

Extra options specified below

mkdir -p expression/stringtie/de_novo/
cd expression/stringtie/de_novo/

stringtie --rf -p 4 -l HBR_Rep1 -o HBR_Rep1/transcripts.gtf $RNA_ALIGN_DIR/HBR_Rep1.bam
stringtie --rf -p 4 -l HBR_Rep2 -o HBR_Rep2/transcripts.gtf $RNA_ALIGN_DIR/HBR_Rep2.bam
stringtie --rf -p 4 -l HBR_Rep3 -o HBR_Rep3/transcripts.gtf $RNA_ALIGN_DIR/HBR_Rep3.bam

stringtie --rf -p 4 -l UHR_Rep1 -o UHR_Rep1/transcripts.gtf $RNA_ALIGN_DIR/UHR_Rep1.bam
stringtie --rf -p 4 -l UHR_Rep2 -o UHR_Rep2/transcripts.gtf $RNA_ALIGN_DIR/UHR_Rep2.bam
stringtie --rf -p 4 -l UHR_Rep3 -o UHR_Rep3/transcripts.gtf $RNA_ALIGN_DIR/UHR_Rep3.bam