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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 Geo,
In my BAM file, there is a certain number of spliced read alignments which do not have the XS tag. My understanding is StringTie will ignore those spliced read alignments which do not hav…
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Hi Ian,
Thanks for making this great tool available!
I've been able to get this running in a Singularity container on my machine, but I would like to have output in GenBank format (I can't find an…
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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…
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Hi,
Thanks for this super nice method and the pipeline. In the minimap2 bam outputs, I don't see any junction reads even though minimap2 is run with the `-x splice` parameter. Sashimi plots are all…
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Hello,
My problem relates to the case in which the user invokes the 'MafIndex.get_spliced' method in the case of multiple negative strand exons.
I use the following example:
**Single Exon**
…
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Hey!
I got one question: the `pufferfish align` command has a `--genomicReads` parameter, which I assume activates a non-splice alignment mode. However the README says that spliced-alignment is not…
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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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Just in megalodon, where you can pass custom settings to guppy, it would be nice to be able to pass custom mapping settings to minimap/mappy. For example, for things like spliced alignment and tuning …
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# To Do
- [x] Literature review of spliced short read alignment methods (is anyone using Minimap2?)
- [x] Review Rust libraries for alignment and minimizers
- [x] Make stand-alone command line Ru…