-
Hi, I'm using gffcompare to generate a combined transcripts file from multiple resources. I'm wondering whether we could keep the CDS entry from each resource in the combined.gtf file? It's probably n…
-
Hello,
After running the ORFQuant pipeline and looking at the candidate ORFs in the gtf file, it looks like ORFs with exons overlapped with an adjacent cds region are being merged together resultin…
-
Hi,
The tool says that it can work with GFF3. But it only works with GTF. Can we get GFF3 support?
Er…
-
Currently, UTR region inference works only for non-spliced UTR regions:
https://github.com/kipoi/kipoiseq/blob/e67fab64ce5306b0f5a39557a93c768f5ab733f6/kipoiseq/extractors/gtf.py#L348-L368
**TODO:…
Hoeze updated
3 years ago
-
Hello,
When I run other species, it works well. But when I run the wheat genome, it got an error like that:
...
Merging reference and test GTF files
2018-07-19 20:26:08,258 - root - INFO - Adding …
-
Hi Geo,
I have nanopore cDNA data aligned with minimap2 (with --cs --MD). I tried abundance estimation with StringTie v1.3.5 that should recognize the "CS" tag as an alternative to "XS". The splice…
-
Hi,
My Finder crashed during FindCDS at the codan steps. Codan throw an error about duplicate key :
```
ValueError: Duplicate key 'chr6:1-94332053.99_10_covsplit.0'
```
After checking this error,…
-
Datashader supports shading multiple attributes of each pixel in different colours. I wonder if we could shade num_inheritors as another dimension? Might take some fiddling, but the examples here look…
-
Hi,
running
```
nf-core/slamseq v1.0.0
Container: singularity - nfcore/slamseq:1.0.0
```
leads to
```
Error executing process > 'gtf2bed (genes.gtf)'
Caused by:
Process `gtf2bed (gene…
-
Consider a small target panel covering the exons of a few dozen genes, but both introns and exons of one gene that is frequently amplified in test samples. The log2 coverage values used for GC and oth…