User: Ctanes

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Ctanes70
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Location:
United States
Last seen:
5 years ago
Joined:
7 years, 9 months ago
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c*****@gmail.com

Posts by Ctanes

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Comment: C: discrepancy in the rehh results
... Here is the link to the paper. http://www.plosbiology.org/article/info%3Adoi%2F10.1371%2Fjournal.pbio.0050171 It is the integrated Site Specific EHH and used for the pairwise population test (Rsb). I am not using Rsb yet for my research but I am more focused on the IHH (Integrated EHH) and the with ...
written 5.1 years ago by Ctanes70
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discrepancy in the rehh results
... Hello, I am using the R package rehh to find SNPs that are undergoing positive selection in genomic regions of interest using the HapMap data. However I am having issues with the consistency of the results. If I have two overlapping regions: Chr1:151.8Mb-153.3Mb and Chr1:152.3-154.4Mb, the IHH, iES ...
selection rehh ihh population genetics written 5.1 years ago by Ctanes70
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Answer: A: How to deal with cross-hybridizing Affymetrix (or other) probe sets?
... I would recommend using custom cdf files. They redefine the probe sets so that it's one to one mapping to the genes. I worked with Affymetrix arrays and use the cdf files here: http://brainarray.mbni.med.umich.edu/brainarray/default.asp They keep a very good update of their cdf files as new mRNA inf ...
written 5.2 years ago by Ctanes70
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Comment: C: dbSNP b126 in vcf format
... Thank you for your answer. In that case I think it might be easier for me to liftover the hapmap data to hg19 since most population tools out there are geared towards 100 Genomes and already have the supporting data available for hg19 build. ...
written 5.2 years ago by Ctanes70
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dbSNP b126 in vcf format
... Hello everyone, I am trying to find dbSNP build 126 in vcf format so that I can use it to analyze HapMap data. dbSNP directs me here: ftp://ftp.ncbi.nlm.nih.gov/snp/, but I can't find the older versions in vcf format to download. Does anyone know where I can find it? Thank you in advance! ...
hapmap vcf dbsnp written 5.2 years ago by Ctanes70 • updated 5.2 years ago by Daniel Swan13k
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Ncbi Taxonomy Database In Xml Format
... I would like to get the full lineage tree downstream of a phylum (all the subcategories until species level) in xml format from the NCBI Taxonomy database. I tried using ncbi eutils: http://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=taxonomy&id=1239&retmode=xml however that search ...
xml taxonomy written 6.2 years ago by Ctanes70 • updated 13 months ago by Biostar ♦♦ 20
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Converting Entrez Ids To Genomic Intervals In Galaxy
... As part of a project, I need to use cistrome Galaxy to convert Entrez IDs to genomic intervals. I uploaded the EntrezID list in tabular format, but I'm having trouble getting the corresponding chromosome list. Can someone help me out? ...
galaxy entrez written 7.8 years ago by Ctanes70 • updated 6.3 years ago by Biostar ♦♦ 20

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