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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
3 months ago
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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…
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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…
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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
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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 …
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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…
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Update the following URL to point to the GitHub repository of
the package you wish to submit to Bioconductor
Repository: https://github.com/omicscodeathon/rhinotypeR
Confirm the following by edit…
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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`
…
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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…
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For first round of integration testing with Kids First, we need the priority 1 fields from sequencing (and maybe 2). These fields include:
### Priority 1
seq_filename
analyte_type
sequencing_…