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Hi Ivan,
we tested Graphmap to align RNA-seq reads to the reference genome. For benchmark purposes, we tried to align the [reference transcripts](ftp://ftp.ensembl.org/pub/release-89/gtf/drosophil…
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It may be worth trying [miniprot](https://github.com/lh3/miniprot) for spliced alignments as an alternative path for generating these exon support results.
Though in my tests I found it didn't alwa…
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This is a very cool project! There is a use-case for which we often have a need, and I wonder if it's enabled by `impg`.
Say I have an a collection of (RNA-seq) reads aligned against the genome (…
rob-p updated
3 months ago
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Hi,
When I used nanopolish call methylation, there was an error as follow:
Error: spliced alignments detected when loading read cce11e44-9f88-45f8-8fa4-5fdf23314323
Please align the reads t…
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Hello vg team
It is amazing the work you are doing.
I am relatively new to using vg and I would appreciate a little help with my question please.
I want to download an already constructed human pa…
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Hollo, thanks for this useful tool!
I used Hisat2 (version 2.2.1) to map metatranscriptomics reads to a specific prokaryotic genome.
When the command was ` hisat2 -x index/prokaryotic -1 paire…
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Hi,
I would like to report (what seems to be) a bug with with MafIO.get_spliced function. Here is the output of running system information script suggested in the issue template:
> 3.8.5 (defa…
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Hello,
I'm very new to STAR and linux in general. In order to use Braker for gene annotation, I am trying to receive a spliced alignment using STAR. (I have PacBio data).
This is my command:
**modu…
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Hi,
I am getting an error with the ProtHint step and I'm not sure what the cause of it is. Could it be because it couldn't find enough memory or something?
`error: ProtHint exited due to an err…