User: JMR

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JMR120
Reputation:
120
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Location:
London - United Kingdom
Last seen:
3 years, 7 months ago
Joined:
3 years, 11 months ago
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Posts by JMR

<prev • 20 results • page 1 of 2 • next >
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Comment: C: A Database Of Signatures Of Selection In The 1000 Genomes Dataset
... From the supplemental information:  Raw scores from ΔiHH, iHS and XP-EHH were standardized in bins of derived allele frequency (step size of 0.05) using the respective genome-wide distribution for each statistic to capture signal from ancestral SNPs that have hitchhiked to high frequency along with ...
written 3.6 years ago by JMR120
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Comment: C: A Database Of Signatures Of Selection In The 1000 Genomes Dataset
... iHS scores are usually given as absolute values, hence all positives. The negative or positive value that this statistics can give will also depend on the equation used. On the original Voight et al (2006) paper, negative values indicated selection at derived alleles for instance. Also unstardardise ...
written 3.6 years ago by JMR120
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Cross population tests for detecting signals of positive selection: Rsb or XP-EHH?
... I am working on dense genotype data trying to detect signals of positive selection. I recently estimated the iHS statistic of my sample using the rehh package in R. Now I also want to try another test. I've seen publications using, besides iHS, the XP-EHH statistic and Rsb which are both based on e ...
selection snp written 3.6 years ago by JMR120 • updated 3.6 years ago by Biostar ♦♦ 20
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Comment: C: How to get ancestral SNPs states for GRCh37.p13
... I am going to try that after checking how many SNPs with ancestral information are there on the dbSNP dataset. Thanks. ...
written 3.8 years ago by JMR120
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Comment: C: How to get ancestral SNPs states for GRCh37.p13
... Hi Siva, I just encountered another problem. For several rsSNPs I found that different batches point to different ancestral alleles. Will batch number should I trust? The latest one? I searched for information on batches on the dbSNP website but couldn't find anything. ...
written 3.8 years ago by JMR120
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Comment: C: Tri-allelic SNP genotype
... It will depend on your platform. That's why I said to check the manual for your platform. ...
written 3.8 years ago by JMR120
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Answer: A: Tri-allelic SNP genotype
... Because you are working on a microarray dataset you shouldn't expect to find tri-allelic SNPs. Most platform work only with biallelic SNPs, but you can check the SNP manually using the dbSNP website for example to be sure. Check the manual for your platform as well. If I had to guess your problem c ...
written 3.8 years ago by JMR120
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Comment: C: Getting ancestral states for SNP chip data for running selscan software
... Thanks for the comment. Yes, I checked the reference data and now I am working with the ancestral data for my assembly. Alas, I still got some rsSNPs with two ancestral alleles in that file. I am not sure what that problem could be. Maybe some discrepancies in different outgroups used as ancestral? ...
written 3.8 years ago by JMR120
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Comment: C: How to get ancestral SNPs states for GRCh37.p13
... Thank you so much! This solved all my questions! ...
written 3.8 years ago by JMR120
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Comment: C: How to get ancestral SNPs states for GRCh37.p13
... Thank you so much Siva! I downloaded the new files for GRCh37 and will try to match my rsnumber and physical position to them. I have another question though, b142_SNPChrPosOnRef_105.bcp and SNPAncestralAllele.bcp have different number of rows. Shouldn't they be the same? ...
written 3.8 years ago by JMR120

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Scholar 3.9 years ago, created an answer that has been accepted. For A: Selection detection software

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