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Using rMATS with ONT data #98

Open pchamely-2 opened 3 years ago

pchamely-2 commented 3 years ago

Hi there! I read in this previous issue, that you guys were working on developing a version of rMATS to work with ONT data (https://github.com/Xinglab/rmats-turbo/issues/8) .....Has there been any updates on this effort? We would like to use specifically the annotation function with our ONT data.

EricKutschera commented 3 years ago

We are working on a new tool that is designed for quantifying isoforms using ONT data. That new tool has not been released yet. I do not know exactly when, but we do plan to make the new tool available in the future

pchamely-2 commented 3 years ago

Thanks for the Update! Please do let us know when the tool is released and we are happy to try out any Dev versions you may have

EricKutschera commented 2 years ago

We have released ESPRESSO which is a tool for quantification of transcript isoforms from long reads: https://github.com/Xinglab/espresso

It has been tested with Oxford Nanopore data, but it should also work well with PacBio data

capricy commented 2 years ago

We have released ESPRESSO which is a tool for quantification of transcript isoforms from long reads: https://github.com/Xinglab/espresso

It has been tested with Oxford Nanopore data, but it should also work well with PacBio data

Can the output from this tool be used for rMATS pipeline somewhere?

C.

EricKutschera commented 2 years ago

Here is a description of the ESPRESSO output files: https://github.com/Xinglab/espresso/tree/v1.2.2#output The output of ESPRESSO includes the read counts for each detected isoform in each sample and also a GTF file with the isoform definitions

rMATS uses short-reads to quantify splicing events based on exon counts and junction counts, but ESPRESSO uses long-reads to quantify full length isoforms. rMATS and ESPRESSO are not counting the same things and the ESPRESSO output is expected to be useful independent of rMATS. Maybe in some situation it would be useful to give the GTF file from ESPRESSO as an input to rMATS