-
PR should *only* be used in col2 in the GAF
```
curl -L -s "http://current.geneontology.org/annotations/mgi.gaf.gz" | gzip -dc | grep ^PR | wc
2139 51464 494819
```
Examples:
```
P…
-
Hi Magdoll !
I use SQANTI2 to analyse my pacbio data. In my result, some isoforms was identified as antisense ,but the colum for associated_gene is empty. I read the code, find that line 1049-1074 :…
-
Hello,
I am a Postdoctoral researcher working in Angus Nairn’s lab, Department of Psychiatry, Yale University. We used a proximity labelling proteomics approach to identify the protein interactome of…
-
### Operating System
Other Linux (please specify below)
### Other Linux
Red Hat Enterprise Linux release 8.6
### Workflow Version
v1.1.1-g999fb4e
### Workflow Execution
Command li…
-
From Monical Poelchau:
"One of our annotators is working on a gene model with ~20 isoforms. When attempting to drag more evidence into the user-created annotations track in the area of this gene mode…
-
Hi Liz,
I'm using chain_samples.py on 6 human samples. The 6 samples were multiplexed and run over 6 SMRTcells and samples were combined after the refine step.
After the collapse by isoform step the…
-
Hi team,
I have recently run sqanti3 with fasta as input, and the result table contains some duplicate isoforms.
I had a quick check and found it stems from the `corrected.gtf` file first, which …
-
Hi, I have a set of samples for which I am running FLAIR. Some samples have a unique isoform which make up a substantial fraction of the gene transcript from that specific sample, but only a small fra…
-
Dear Nicolas,
I have tried to run UNAGI on my own nanopore data. I run it successufully without error.
However, I cannot got the strand infomation in the final output (both 'Splicing_Isoforms.bed…
-
Apparently we're not reading these in, though we do read in the protein's annotated modified residues. It may or may not be a good idea to read in all SNVs, etc. but maybe we should provide options to…