-
The reported annotation for peaks that fall in introns (and exons) are frequently reported as being in the adjacent neighboring gene, suggesting an off-by-1 indexing error when reporting the identifie…
-
Hello @giovanniquinones,
I have been trying isoLASER out but I'm failing to generate the output pickle files from:
`isolaser_extract_exonic_parts -g {annot.gtf} -o {transcript.db}`
For the ann…
-
Hello,
Can you fix your code so that the exon colors appear in a real rainbow palette.
The colors for the exons are ordered in this way right now: Ex1, Ex10, Ex11 .... Ex2, Ex20...., when it sho…
-
Hello,
I recently started to use ASpli to quantify the alternative splicing levels of my gene. My gene has 3 isoforms which only differ from each other by one exon.
- The first one has all exons…
-
For genes on reverse strand, the exons are still numerotated in the forward strand order:
![Screenshot from 2024-07-09 18-04-40](https://github.com/Oshlack/Toblerone/assets/20519429/4fdb3628-8969-4…
-
Right now the Excel file could provide more detailed information that is scattered throughout different files. This information should be unified in the produced .XLS file.
Bonus points: can we als…
-
My RNA-seq data were downloaded from the Internet, and the authors did not elaborate on the type of library built. for --libtype parameter, i try two ways.
one: python3 /public/home/xiaoxiong/minic…
-
When `autoplot`ing from an `EnsDb` or `TxDb`, UTR, CDS and exon features are shown as rectangles. This is redundant for protein coding genes, since UTR and CDS features cover all exons. Exons are dr…
-
Hello,
What is the format of the exons bed file as input to ichorCNA?
Thank you,
Sudhir
-
Does it work will with super short exons like a single codon in length?