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**Description:**
Extend the existing mechanism for reusing indices based on md5sums to also reuse spliced alignment information. By calculating and storing the md5sums of the plasmid and reference fi…
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Hello rpvg team
I have a general question and I would appreciate your help.
I am trying to infer the haplotype expression of human-experiment reads using rpvg.
I have performed the construction o…
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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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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, I'm sorry if this is rather elementary.
But I attempted to generate the appropriate input bam files for uncalled4 align via the following command:
`guppy_basecaller -i /fast5_directory -…
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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
4 months ago
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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…