User: andreagarcia871

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Posts by andreagarcia871

<prev • 10 results • page 1 of 1 • next >
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How to read a ".ld.bin" file produced by PLINK
... I have a .ld.bin file produced by PLINK (cannot remember now how it was produced) which I want to plot. This .bin file is about 160Mbytes so I guess it could be really bigger if uncompressed as .ld (I have read that [.ld format is just a table][1]). I cannot find [any documentation][2] in PLINK we ...
R plink ld written 4 months ago by andreagarcia87160
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How to get the HMM file for PennCNV?
... Hi I am testing the PennCNV software using input data from Illumina final report data, and I was able to generate a .PFB file for my samples. However I missed something in the PennCNV [official guide][1] beacuse I couldn't find how to build or obtain the .HMM model file used for cnv call detection. ...
hmm penncnv cnv written 11 months ago by andreagarcia87160
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Comment: C: Confused about Effective Population size
... Thank you Petr, maybe you could reply in the Answer input? So, from what I understand, it almost makes no sense to use an "universal" Ne size when I have my own samples. Also one also should have an estimate population count of a breed for the particular geographical region implicated in the study ...
written 19 months ago by andreagarcia87160
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Confused about Effective Population size
... I am newbie in bioinformatics, I started to read about Effective Population size (Ne) being an important genetic estimation for population studies (my goal is to run SHAPEIT software with the proper effective population size parameter), and I have this kind of basic theoretical question: Let's say ...
shapeit effective population size phasing ne written 19 months ago by andreagarcia87160
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SHAPEIT allele encoding
... My goal is to do phasing using shapeit2 (I don't have haplotype reference panels) and I have .ped and .map files for some populations in A/C/G/T format. AFAIK the .ped file only contains genotypes, but no reference allele information. Shapeit2 generated 2 files: shapeit.v2.r644.linux.x86_64 \ ...
shapeit plink phasing written 3.0 years ago by andreagarcia87160
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Consensus sequence software?
... I am looking for a command line tool to get a consensus sequence, with a proper example usage not from a paper where everything is theoretical or from a software suite. I have reviewed options but quality of answers and documentation is bad. For example there is UGENE but they don't provide a comman ...
consensus sequence written 4.3 years ago by andreagarcia87160 • updated 4.3 years ago by Daniel3.6k
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Does exists a sequence error correction software that uses a MSA result to resolve read errors at specific SNP positions?
... I have an input DNA sequence with read errors (bases appear as [A/G] for example). I have also a multiple sequence alignment of all current alleles reported for a gene in a specific region of interest. Now I want to find which combination of alleles in the MSA explains the combination of polymorphi ...
correction sequence alignment msa written 4.4 years ago by andreagarcia87160 • updated 4.3 years ago by Soumitra Pal10
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What's the difference between generating all possible genotypes from a MSA and extracting a consensus sequence?
... I have seen examples of getting a consensus sequence by using software like UGENE or JalView. Now what would be an example output of generating all possible genotyopes from a Multiple Sequence Alignment result?   ...
consensus genotypes msa written 4.4 years ago by andreagarcia87160 • updated 4.3 years ago by Josh Herr5.6k
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Comment: C: Where To Find Huge Sample Files? (Phylip, Nexus, Clustalw, Etc)
... Edited with links to some sample files of what I'm looking for. I just want the same files but with many more samples. ...
written 6.0 years ago by andreagarcia87160
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Where To Find Huge Sample Files? (Phylip, Nexus, Clustalw, Etc)
... I'm developing a parser for interleaved file formats, like Phylip, ClustalW and Nexus. But a challenge is to validate my parser against big samples, and do some stress testing. There are some nice short examples : PHYLIP format, Nexus DNA format. Anyone mind to share URL's to download .phy,. nxs, .n ...
clustalw written 6.0 years ago by andreagarcia87160 • updated 5.5 years ago by brianfoleynm0

Latest awards to andreagarcia871

Great Question 11 months ago, created a question with more than 5,000 views. For Consensus sequence software?
Popular Question 11 months ago, created a question with more than 1,000 views. For SHAPEIT allele encoding
Popular Question 4.2 years ago, created a question with more than 1,000 views. For Where To Find Huge Sample Files? (Phylip, Nexus, Clustalw, Etc)
Popular Question 4.2 years ago, created a question with more than 1,000 views. For Consensus sequence software?
Student 4.3 years ago, asked a question with at least 3 up-votes. For Consensus sequence software?

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