User: Ace

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Ace70
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Posts by Ace

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Why is VCFTools excluding so many SNPs in its Tajima D calculation?
... I used VCFTools to calculate Tajima's D for my population. When I started doing more specific analyses, I found that while VCFTools (via allele freq) recognized 22 SNPs in a certain gene, it was only including 5, total, into all the regions that fell into that area, producing many NA windows. Is thi ...
vcftools snp population genetics written 6 weeks ago by Ace70 • updated 8 days ago by Biostar ♦♦ 20
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Answer: A: PopGenome - readData error
... I know this post is past its prime, but I recently had this same error and thought I'd help out anyone else that happened to come across this post looking for answers. I found that it is resolved by using their "split_into_scaffolds" function, rather than manually splitting as some people have recom ...
written 8 weeks ago by Ace70
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Comment: C: HMMER vs OrthoMCL vs Blast: When to use what for finding gene groups
... So, from your response and that of Jean, it would be ok to use HMMer or blastp to identify a gene family within the same assembly or even a group of assemblies based on domain structure, but you'd want to use something like orthomcl to infer history of the genes? In this case my ultimate goal is t ...
written 3 months ago by Ace70
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HMMER vs OrthoMCL vs Blast: When to use what for finding gene groups
... So, I've seen a lot of people using orthoMCL to extract gene families. I am wondering why I don't see direct searches like blastp and HMMer used more. Is there logic to using OrthoMCL when you already have an idea of what kind of genes you're looking for? ...
similarity gene families blast orthomcl written 3 months ago by Ace70 • updated 3 months ago by Mensur Dlakic2.4k
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Answer: A: finding specific SNPs in VCF files
... If you have a VCF file, vcftools' positions overlap function should work, specifically: > vcftools --vcf $vcf --positions-overlap $list --kept-sites --out $out would give you a file ${out}.kept.sites that would include all the sites in your VCF that are present in your list of snps. You coul ...
written 3 months ago by Ace70
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Answer: A: GATK4 Variant calling with non-human model and no known SNP database
... The GVCF mode in GATK is designed to do variant calling in groups. In theory you should get the same result doing a direct HC and doing the gvcf mode, it's just that the latter allows you to skip some time if you add samples in or want to use a different combination later. You want to make a g.vcf ...
written 3 months ago by Ace70
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Controlling for batch effect in SNP-based PCA
... I'm trying to combine data from 4 studies with my own in order to add context to my data. There are some variations in regional collection that I want to highlight, but study differences seem to dominate the first and second eigenvector of my PCA, which makes me worry the batch effect could be beyon ...
batch effect pca snp whole-genome written 4 months ago by Ace70
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Comment: C: PCA cannot separate different breeds
... How were these samples collected and processed before variant calling? What variant calling filters did you use? There could be alternative sources of variation that are taking over your first two principal components. What percentage of variation do your PCs explain? If this number is quite low, ...
written 4 months ago by Ace70
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Comment: C: How to annotate FASTA genome using GFF genes from another genome?
... What genome are you working with? You can create Embl files from gff (look for gff to embl converter scripts), as well. ...
written 4 months ago by Ace70
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Comment: C: Why am I getting fewer variants with more samples?
... As an update, I did post this on GATK forum https://gatkforums.broadinstitute.org/gatk/discussion/24163/larger-sample-sizes-are-reducing-snps-dramatically However, I noticed looking through some VCF files that the caller is only registering chromosome 1 so my new challenge is tracking that down. ...
written 5 months ago by Ace70

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Scholar 7 months ago, created an answer that has been accepted. For A: GATK HC mis-reading chromosomes

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