Hello all,
I am wondering if anyone here has any experience trying to use Isoseq outputs with MAJIQ-L.
Isoseq is the standard pipeline, built and maintained by PacBio, for processing their long read data. I cannot seem to get MAJIQ-L to parse the information correctly compared to outputs I generated using the Isoquant pipeline. When running the prerequisite commands prior to running the viewer, everything runs smoothly with no errors. However, once I run the view command, the view opens as if long read data has been parsed but no reads can be seen.
I understand there will be differences since Isoseq and Isoquant are two different algorithms and I've done the necessary comparisons to ensure that I am not just looking at a gene thats detected by one pipeline and not the other.
I did have to do some manipulation to the needed Isoseq files. Namely, converting the gff to a gtf and extracting the isoformID and counts column to their own csv file.
Any feedback or thoughts would be appreciated. Yes, I could simply use Isoquant for all of my analyses moving forward, but Isoseq is considered more robust and accurate at this time so I would love to be able to use data generated from that pipeline over all else.
Thank you in advance for your help and to the developers for this tool!
Tayvia Brownmiller