Andrey Prjibelski
Andrey Prjibelski
@sparthib This issue should be now resolved starting version 3.5.0.
Dear @ccmeth Each line in read_assignments contain only a single read assignment to a single known isoform. Thus, all event are related only to one isoform indicated in column 4....
@ccmeth The original visualization issue should be fixed now in [IsoQuant 3.5.1](https://github.com/ablab/IsoQuant/releases/tag/v3.5.1).
Dear @ljwharbers Yes, visualizer was not designed to work with the linear format, and the option was introduced later without properly adapting `visualize.py`. Thank you for bringing our attention -...
Dear @BenneyMRArgue Thanks for the feedback! I would recommend you to try the latest IsoQuant version (3.5.2). It has far better RAM consumption compared to 3.4.1 - a major problem...
@vasikara17 Thanks for the feedback! Could you please clarify, would you like to have a separate output for each condition, or an expression table with barcodes and conditions? How are...
Okay, following your post in https://github.com/ablab/IsoQuant/issues/211 So far IsoQuant supports only one way of grouping reads via `--read_group`, so either by condition or by barcode. This can be done using...
Dear @sanyalab IsoQuant does support both GTF and GFF, but not BED. Could you send me the entire isoquant.log file? Also, you can try running IsoQuant with `--no_gtf_check`. Best Andrey
@sanyalab Thanks a lot! I will add GFF3 support to the internal checker. So if gffutils converted it, you can run IsoQuant with `--no_gtf_check` as well.
GFF3 should work in IsoQuant 3.6.1 without warnings.