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The new tuxedo suite consists of three tools for transcript-level analysis of RNA-Seq data:
- HISATHISAT2: Spliced alignment of reads to the genome
- Stringtie: Assembly of transcripts based on mapping to genome, including novel transcripts. Quantification of these transcripts.
- Ballgown: Identification of differentially expressed genes and transcripts.
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-p brings up a key concept when submitting jobs on TACC: wayness. Go back to Submitting Jobs to Lonestar5Lonestar6 for more.
OUTPUT: Each stringtie command generates a new gtf file, so you will have one for each sample.
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