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I have a list of dbSNP rsIDs for GRCh37 and I want to convert them to the equivalent IDs in GRCh38. This is using the most recent dbSNP build (150...
Asked on 09/01/2020 by Rob John
4 answerI am reading Section 5.2, Kinship and Inbreeding Coefficients, of Kenneth Lange, Mathematical and Statistical Methods for Genetic Analysis. There the kinship coefficient $Phi_{i,j}$ is defined...
Asked on 08/31/2020
2 answerI am attempting to create a markerInfoFile for use in a program called popSTR (GitHub Documentation: https://github.com/DecodeGenetics/popSTR). The marker info file should contain information about microsatellites in...
Asked on 08/30/2020 by annabelperry
0 answerI have some sequences shown belowCAGGTAGCCCCGGTCAGAAGGGTTTGATTGGTGAGGCAAGTATGAACTGTATGCCTGGTAACCTATGTACTGGCTGTGAGACAGGTGGGCTCAGTGAGAGGGGTGAGTTGGGTATGTGAGGTGAGACAGGTGGAGEach line has 9 nucleotides.Consider it to be 9 columns.I want to calculate the nucleotide frequency of each nucleotide for each of the...
Asked on 08/19/2020 by user3138373
7 answerI am new to the Seurat package and was looking at the tutorials on the Seurat website and am just curious to know if there is any way to perform...
Asked on 08/11/2020 by vdu12345
1 answerWhat is the quickest way to calculate the number of chemical reactions present in each pathway for a given organism and which online database such as Kegg,...
Asked on 08/11/2020 by MMphysics
0 answerHi im looking for the aligned bases in the reads for a given reference position. im using the following script from the pysam documentataion.I adjusted it to find the...
Asked on 08/08/2020 by Diesel__100
0 answerI have a nexus formatted BEAST output containing 20,000 phylogenetic trees of seven taxa. Is there any way to get the percentage of each unique phylogenetic tree contained...
Asked on 08/08/2020 by Justine Vandendorpe
2 answerMaximum Likelihood analysis compares the tips or the species based on their sequence similarity while Parsimony analysis compares the characteristic features among the species. So far I did comparison of...
Asked on 08/05/2020
2 answerHow can I convert a VCF file into a genotype table (SNP matrix)? I have this format:##fileformat=VCFv4.0##fileDate=20200722##source=test##reference=test##FILTER=<ID=PASS,Description="All filters passed">##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Read Depth">##FORMAT=<ID=DV,Number=1,Type=Integer,Description="Number of high-quality non-reference bases">##FORMAT=<ID=GQ,Number=1,Type=Integer,Description="Genotype Quality">#CHROM POS ID ...
Asked on 07/30/2020 by snowflake
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