-
We would like to verify whether there is a significant difference in efficiency of the hm pipeline for seq GWAS.
1. Calculate the average % of dropped and unable to harmonise variants among a repres…
ljwh2 updated
4 months ago
-
Greetings. Thank you for developing Geny to expand the potential of the KIR genotyping with next-generation sequencing data!
In your manuscript, you also compared the accuracy with T1K, and I appr…
-
Hi, @eblerjana
I found that several samples's peak is wrong according the pangenie log. So would you mind teliing what's the influence of these peak? Is there any way to set peak?
Here is a ex…
-
Thanks for creating this extraordinary tool. Currently, our lab found a VNTR loci by long read sequencing data, and is really looking forward to validating our finding by genotyping it in sea-like NGS…
-
Requested in #311 by @jcgrenier:
> Another useful QC that could be integrated would be one using Genotyping array data. As sometimes we like to do analysis like eQTL analysis and use both genotypin…
ewels updated
3 years ago
-
Hi,
I am a molecular biologist. Briefly, I am working on a non-model species, with no genomic data. I have some Genotyping-By-Sequencing data from different populations and I want to use npGeno to …
-
Hi there
Congratulations on a very nicely written paper. I'm still absorbing it, but I wondered what I ought to do if using it on small genomes. Your documentation says you need 1 million SNPs in y…
-
Here is an outline of a workflow that needs to be enabled in Galaxy to allow variant calling on HIV-1 datasets
- [ ] Upload all datasets for `PRJNA517147`
- [ ] QC with `fastqc` and `multiqc`
…
-
Is there any guidance for using Genotyping-By-Sequencing targeted panels like [twist](https://www.twistbioscience.com/products/ngs/alliance-panels/diversity-snp-panel) ?
I thought perhaps doing a l…
-
Hi,
In your paper, you say that you "discard those reads with low alignment quality, including MAPQ < 20, aligned length < 30 nt and FLAG with UNMAP, SECONDARY, QCFAIL (and DUP if UMI is not applic…