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kvittingseerup / IsoformSwitchAnalyzeR

An R package to Identify, Annoatate and Visialize Isoform Switches with Functional Consequences (from RNA-seq data)
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working with quantification tools that detect novel isoforms #244

Open sparthib opened 1 month ago

sparthib commented 1 month ago

For tools such as bambu and isoquant, they produce an extended gtf including the novel isoforms which are not accompanied by a fasta file containing the sequence information. Is the fasta file required to create a switch plots? I'm just trying to understand more the role of the reference fasta file in IsoformSwitchAnalyzer , thank you!

Sowmya

chunxubioinfor commented 1 month ago

Hi Sowmya, the fasta file is optional while creating the switchAnalyzeRlist. As you have the gtf file, you can follow this to get the fasta sequences: https://www.bioconductor.org/packages/release/bioc/vignettes/IsoformSwitchAnalyzeR/inst/doc/IsoformSwitchAnalyzeR.html#what-transcript-database-should-i-use And after this, you could perform external analysis and create switch plots. :)