Research Object Crate for Find transcripts - TSI

This is part of a series of workflows to annotate a genome, tagged with `TSI-annotation`. These workflows are based on command-line code by Luke Silver, converted into Galaxy Australia workflows. The workflows can be run in this order: * Repeat masking * RNAseq QC and read trimming * Find transcripts * Combine transcripts * Extract transcripts * Convert formats * Fgenesh annotation **** About this workflow: * Run this workflow per tissue. * Inputs: masked_genome.fasta and the trimmed RNAseq reads (R1 and R2) from one type of tissue. * Index genome and align reads to genome with HISAT2, with default settings except for: Advanced options: spliced alignment options: specify options: Transcriptome assembly reporting: selected option: Report alignments tailored for transcript assemblers including StringTie (equivalent to -dta flag). * Runs samtools sort to sort bam by coordinate. * Runs StringTie to generate gtf from sorted bam. * Output: transcripts.gtf from a single tissue.

Author

Anna Syme

License

GPL-3.0

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