Adding transcriptome in a TALON-independent way?

[lscdanson]

Hi your tutorial page mentioned that users could use other tools that yield transcriptomes as input to Swan; however, I saw that in the step of "Adding transcript models from a GTF", a gtf file ("all_talon_observedOnly.gtf") seems to be generated from TALON. I wonder if you could suggest a way to do the same without the need to use TALON. Many thanks!

[fairliereese]

Hi! The GTF is the common format that you can use as input. It does not have to be generated from TALON!

[lscdanson]

Thanks for your prompt reply. Sorry if I've misunderstood as I'm new to this. To my knowledge, a gtf file usually refers to the annotation gtf file, which has already been supplied in the previous step via sg.add_annotation(annot_gtf). I downloaded mine from Ensembl (https://ftp.ensembl.org/pub/release-111/gtf/homo_sapiens/). May I know what this transcriptome gtf is and where else can I obtain? coz I don't seem to see any other GTF-formatted file from my pipeline outputs. Thanks so much!

[fairliereese]

Ah I see. If you are not doing transcript discovery in your data processing, you don't need to add another transcriptome GTF file, as all of the transcript that you're detecting are already from the Ensembl GTF you've mentioned. This is a characteristic I'd expect from a short-read RNA-seq data processing pipeline, am I correct in assuming this? If you are using long-read RNA-seq data, what are you using to process it?