Bioinformatic tools online - Running the StringTie pipeline
In this video, I show you, how you can do a StringTie analysis with "Bioinformatic tools online" We start from sorted bam-files and first run StringTie to identify new isoforms. Those are saved in sample specific reference files. The reference files are then merged with StringTie --merge to get a unique reference for all samples. Then we re-run StringTie to get TPM and FPKM-values from the known and new transcripts and to get input-files for Ballgown. Finally, we use Ballgown to calculate differentially expressed genes and transcripts.