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I have the following Stringtie RNA-seq output files for several samples in the image below.

For additional context, I have utilized as part of my RNA-seq workflow.

  • HISAT2,
  • samtools, and
  • Stringtie

Additionally I need help with trying to analyze mRNA transcript isoforms as I am completely new to this type of analysis.

Questions Which file outputs should I use and what additional tools/software should I use to analyze mRNA transcript isoforms?

Any help is much appreciated!

HISAT2 Output Files Per Sample.

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