Isoform Analysis: StringTie creates .tsv value that has null values for every gene id
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11 months ago

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

STAR bash StringTie RNA-Seq • 555 views
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hi,while aligning with STAR did you given --outSAMstrandField intronMotif

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