User: Ctanes
Ctanes • 70
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- United States
- Last seen:
- 5 years, 10 months ago
- Joined:
- 8 years, 6 months ago
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Posts by Ctanes
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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 5.9 years ago by
Ctanes • 70
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... 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 ...
written 5.9 years ago by
Ctanes • 70
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... 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 6.0 years ago by
Ctanes • 70
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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.
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written 6.0 years ago by
Ctanes • 70
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... 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!
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written 6.0 years ago by
Ctanes • 70
• updated
6.0 years ago by
Daniel Swan ♦ 13k
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... 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 ...
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... 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?
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