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I am working on a population genetic project for a fungus with a haploid genome. I am wondering if GONE is suitable for estimating Ne for haploid species?
Thanks!
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Hi,
Recently I have been processing some haploid vcf files from HipSTR output and I find I can't merge haploid data through mergeSTR, and the errors are as follows:
TypeError: ufunc 'isnan' not …
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Hi all,
my genome size is 400Mb with high heterozygosity, so after assembly by falcon with 100X pacbio data,
it produces about 800Mb result, this result maybe is the diploid genome result ,so how to …
moold updated
9 years ago
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I propose to specify it explicitly in the spec that in case of haploid genotype, BCF record should have unphased GT field. It's not a big deal, but current spec leaves some space for uncertainty witho…
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Hello.
As a test I ran GTShark on chrX of 1KGP3 (available from the FTP link below) ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/release/20130502/ALL.chrX.phase3_shapeit2_mvncall_integrated_v1c.20130502.…
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Hello,
I want to run the diploid portion of the pipeline to identify/remove alternative haplotypes if i want a haploid representation of the hybrid genome,should I run the `awk -f ${path_to_3ddna}/ut…
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Hello, I have 3 samples I'm working with. By comparing the total ONT sequenced read length and the estimated haploid genome sizes
sample 1: 24.96x coverage
sample 2: 22.36x coverage
sample 3: 22.47…
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**Is your feature request related to a problem? Please describe.**
The problem is that pixy seems unable to handle sex chromosomes. For example, the X chromosome is homogametic and thus haploid in ma…
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Hello, the species I studied is haploid. After using hifiasm software to assemble hifi and ont data, the test.bp.p_ctg.gfa results showed that the genome size was correct and there were more contig. G…
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We should find out if users would expect to retrieve "increased RNA level"
on a search for "increased gene expression".
108 | increased gene expression (FYPO:0006548) [single locus haploid genotyp…