User: sonia.olaechea

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Posts by sonia.olaechea

<prev • 48 results • page 1 of 5 • next >
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1000Genomes exome vcf
... Hi everyone! I would like to download 1000Genomes exome data for some African populations which I have found in [this repository][1]. However, these are only stored in `cram` format, so I was wondering if they can be found in `vcf`format somewhere else. Any help will be appreciated. Thanks in advanc ...
vcf 1000genomes exome written 5 months ago by sonia.olaechea140
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Comment: C: PGDSPider VCF to BAYENV
... Hi Brian! for me it was something super silly: in the population file I had spaces instead of tabs between the columns (or the other way around, I don't remember...)! Maybe it is your problem as well. Also, I remember that I played around with the `.spid` file. For the VCF to Bayenv conversion there ...
written 5 months ago by sonia.olaechea140
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qvalue for PBS
... Hi everyone, I've calculated PBS values for my SNPs and now I would like to test their significance using the `qvalue` package in R. This package asks you for either a list of p-values or (if you don't have them) to calculate them from a null distribution of your data with the function `empPvals`. M ...
R qvalue pbs written 6 months ago by sonia.olaechea140
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Comment: C: align specific region of human to panTro6
... And another question @JC : I have done the lift over and I'm having a look at the sequences with `UGene` (similar to `Bioedit`). I see now that a big part of panTro6 sequence is displaced just by 1 or 2 nucleotides in some regions. My next step will be to calculate the divergence between both specie ...
written 7 months ago by sonia.olaechea140
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Comment: C: align specific region of human to panTro6
... I would like to eliminate from my human fasta those positions that don't have a match with the panTro fasta. ...
written 7 months ago by sonia.olaechea140
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Comment: C: align specific region of human to panTro6
... Okey! I hadn't heard about LiftOver, but that's exactly what I need! Thank you so much! ...
written 7 months ago by sonia.olaechea140
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align specific region of human to panTro6
... Hi everyone! I'm trying to efficiently align a fasta file with a human sequence to panTro6 sequence but I'm not sure on how to avoid the gaps between both species. Are there tools that take these gaps already into account? Thanks in advance for the help! ...
pantro6 alignment written 7 months ago by sonia.olaechea140 • updated 7 months ago by JC12k
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Comment: C: twoBitToFa retrieving longer sequence than expected in hg19
... Thanks to both of you, you were both right!! It turns out that my `bash command` was counting both the `N's` and the header line of the sequence!! ...
written 7 months ago by sonia.olaechea140
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twoBitToFa retrieving longer sequence than expected in hg19
... Hi all! I'm using twoBitToFa to retrieve a specific region of a chromosome in hg19. The command I'm using is: twoBitToFa http://hgdownload.cse.ucsc.edu/gbdb/hg19/hg19.2bit myfile.fa -seq=chr1 -start=891021 -end=125030866 I would expect there to be 125030866 - 891021 = 124139845 nucleotides. ...
twobittofa hg19 written 7 months ago by sonia.olaechea140 • updated 7 months ago by wm490
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Comment: C: Converting ms or msms output to PLINK or VCF files
... Hello! I'm facing the same issue as well... I've tried to use `ms2geno` but haven't managed to make it work properly. Has anyone found a better option? ...
written 7 months ago by sonia.olaechea140

Latest awards to sonia.olaechea

Popular Question 5 months ago, created a question with more than 1,000 views. For mean Tajima's D value
Popular Question 6 months ago, created a question with more than 1,000 views. For 1000Genomes population allele frequencies for list of SNPs
Popular Question 14 months ago, created a question with more than 1,000 views. For 1000Genomes population allele frequencies for list of SNPs
Popular Question 16 months ago, created a question with more than 1,000 views. For Error: Line 2 of .ped file has more tokens than expected.
Popular Question 16 months ago, created a question with more than 1,000 views. For vcftools --TajimaD in sliding windows

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