stringtie

Transcript assembly and quantification for RNA-Seq data

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Transcript assembly and quantification for RNA-Seq

stringtie

Assemble transcripts from a BAM file$ stringtie -o transcripts.gtf input.bam

Assemble with reference annotation and estimate abundance$ stringtie -G reference.gtf -o transcripts.gtf -A gene_abundances.tsv input.bam

Merge GTF files from multiple samples$ stringtie --merge -o merged.gtf sample1.gtf sample2.gtf sample3.gtf