SQANTI-Reads and General Workflow question

[mpizzagalli777]

Hi all, I have a general question regarding a workflow I have been working on. In order to study alternative splicing and novel transcripts in a series of patient derived cells, I want to generate a high confidence transcriptome. To this end, I have been using SQANTI as my last step. Currently my workflow (per cell line) is as follows: Pychopper on individual LR samples, followed by FLAIR align and correct. After that, I perform FLAIR collapse on the concatenated bed files and pass the gtf output into SQANTI, where I include some SR data as orthogonal support. However, I recently saw SQANTI-reads and was wondering if this approach is incorrect?

Finally, I would like to eventually create a universal transcriptome for these samples. I have four cell lines and triplicates from LR data for each sample. How would I go about generating this combined transcriptome? It seems that using the concatenation and FLAIR collapse approach would allow me to do this but would prevent me from using SQANTI-reads as that requires SQANTI-QC to be run on each individual sample. I would like to create this universal transcriptome in order to ensure that any novel transcripts that appear across cell lines will have a common name between cell lines.

Thanks in advance for any help :)