Hi everyone, I am new to bioinformatics and Biostars as a whole. I am doing isoform analysis on some samples and I've come across a problem. The following code is what I used for StringTie. The resulting .tsv file had 0 values for every gene. I originally thought thought the .bam files from my STAR alignment were empty/non-viable. I double checked this in IGV and there are indeed reads mapped. How can I modify my stringtie code to avoid this problem?
stringtie -p 8 -G reference_genome_pwd -e -B -o pathways/transcripts.gtf -A pathways/gene_abundances.tsv pathways/SAMPLE1/SAMPLE1.bam