EduEyras
commented
12 months ago Hello,
it would be better to use one single GTF file, so that you can compare events across conditions.
You will also need an expression file for each sample based on that GTF. Using your isoseq reads, can you produce a quantification for the transcripts in your consensus GTF?
I hope it helps
Best
Eduardo
On Mon, 27 Nov 2023 at 17:48, Yao Gao @.***> wrote:
I use isoseq3 and pigeon to process mas-iso-seq data. How can I continue to use suppa to analyze the output files obtained. image.png (view on web) https://github.com/comprna/SUPPA/assets/62972588/04af2850-5533-4685-9c4d-26fd22c05281 image.png (view on web) https://github.com/comprna/SUPPA/assets/62972588/124f7851-5209-46c8-bda5-891429978974
I used isoseq3's workflow and got a gff file for each sample, but suppa only requires one gff. Should I combine these gffs, or use individual gffs for each sample to calculate psi.
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I use isoseq3 and pigeon to process mas-iso-seq data. How can I continue to use suppa to analyze the output files obtained.
I used isoseq3's workflow and got a gff file for each sample, but suppa only requires one gff. Should I combine these gff, or use individual gff for each sample to calculate psi.