User: Ace

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Ace60
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Posts by Ace

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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 2 days ago by Ace60
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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 days ago by Ace60 • updated 3 days ago by Mensur Dlakic570
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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 10 days ago by Ace60
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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 11 days ago by Ace60
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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 13 days ago by Ace60
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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 weeks ago by Ace60
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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 5 weeks ago by Ace60
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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 8 weeks ago by Ace60
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Answer: A: how do you download a single SNP in vcf format?
... you could filter it with vcftools > vcftools --vcf $vcf --positions SNP_list.txt --recode --out $out or > vcftools --vcf $vcf --chr $chr --from-bp $start --to-bp $end --recode --out $out The advantage of that is that it will also work with gzvcf or for multiple SNPs, but honestly, it' ...
written 8 weeks ago by Ace60
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Comment: C: Why am I getting fewer variants with more samples?
... Sounds like a good idea. This is before filtration but I have a couple more things I'm trying this evening and if they don't pan out I'll post on GATK tomorrow and report back. In the meantime, do we still have an archive of the other discussion? I'd love to see what logic people came up with. ...
written 9 weeks ago by Ace60

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Scholar 3 months ago, created an answer that has been accepted. For A: GATK HC mis-reading chromosomes

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