-
```
We would be good to have a system to extract the data from AcypiCyc and
collect them in a txt like annotation file with one line per gene (ACYPI)
to use for manual analysis and microarrays annotat…
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I try the "PASTA vignette", and get a error as fowllowing:
######################## code
pbmc dense coercion: allocating vector of size 3.1 GiB
3: In .M2v(x) : sparse->dense coercion: allocati…
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I was looking at the gene annotation files, in particular, http://courtyard.gi.ucsc.edu/~mhauknes/T2T/t2t_Y/annotation_set/CHM13.v2.0.gff3
It looks like the file contains multiple problems, mostly to…
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Hi,
Thanks very much for this program. I've a strange problem: I used mikado transcripts and a close relative to annotate a genome, but unfortunately, I get multiple genes for the exact same locatio…
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Hi,
We've been running BioTraDIS on a .embl file which contains a chromosome and two plasmids ([GCA_000008865.2.txt](https://github.com/sanger-pathogens/Bio-Tradis/files/10115303/GCA_000008865.2.t…
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Hi there!
I want to use Manatee to characterize the ncRNA profile in pigs. I have run several times the perl script changing parameters and I always obtain 0 counts for all the species included in …
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Hi All,
I am running velocyto.py to process the 10x PBMCs data (v3.0.0).
My code is 'velocyto run10x -m cellranger-3.0.0/reference/expressed_repeats_annotation/hg38_rmsk.gtf cellranger-3.0.0/sa…
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### Description of the bug
Hello,
I am having trouble with the sample input file. I have .csv file with correct file names and format as described in the pipeline page (also attached here). I get …
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- [ ] stop-codon missing calculation filter
- [ ] CDS calculation filter
- [ ] Gene models in web apollo gff3 with unmodified coordinates (from #36)
in doc / Common Eukaryotic Annotation Errors
Fr…
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Hi,
I ran all the test data and it worked perfectly. But when I tried to load my own gtf, I got the following error:
```
>genome_annotation gene_overlaps