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Add polishing similar to the approach used in [dragonflye](https://github.com/rpetit3/dragonflye) to generate high-quality chromosomal contigs
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Hi,
While running this
`laml.tnm = trinucleotideMatrix(maf = combined_maf, prefix = 'chr', add = TRUE, ref_genome = "BSgenome.Hsapiens.UCSC.hg18")`
, I got a mistake, like
```
Warning in trinucle…
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-->
**1. What were you trying to do?**
I tried to call vcf for each splitted chromosome after aligning short reads against the variation graph.
**2. What did you want to happen?**
Vcfs for all…
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Some chromosomes have multiple intervals what's the problem, how do you choose them, is there a confidence score.
```
ChrB01 13133334 16966667
ChrB02 48940000 53939999
ChrB03 3341…
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Hello,
In the supplemental information of the BioRxiv preprint (https://www.biorxiv.org/content/10.1101/2023.02.06.527280v2.supplementary-material) I read that over-prediction in small contigs (small…
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Hi,
Can RUTH handle chromosome X? There isn't a mention of it in the manuscript, but the program accepts parameters for sex chromosomes. When I try to load a BCF file containing X-chromosome SNPs, …
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Not sure if it's a feature or bug, but when I try to do interchromosomal with the smaller chromosome on X axis, things go haywire.
E.g. if I load a map and then type the below in the goto box:
6…
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There is no reason to annotate to this directly. You always know the mechanism based on the species
There are 25 direct experimental annotations that could be auto pushed down https://amigo.geneonto…
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chromosomes 1-3 have a difefrent block structure I think and thus break the code:
```
File "/mnt/c/development/varvis-download/development/bamnostic/extract_bam_subset.py", line 111, in
e…
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Hi!
First, I want to say that I really enjoy using SpikeFlow!
I’ve encountered an issue while working with paired-end data. I noticed that some exogenous reads remain in the reference BAM file a…