User: haansi

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haansi50
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Austria
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Posts by haansi

<prev • 6 results • page 1 of 1 • next >
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Answer: A: Mitoseek not installing correctly
... @WouterDeCoster is right - the name of the reference is required to be called "M" or "chrM" - `if (/SN:M|SN:chrM/i) {` see https://github.com/riverlee/MitoSeek/blob/v1.3/mitoSeek_new.pl Another suggestion: you could also try to use lofreq [see previous discussion in biostars][1] [1]: https:// ...
written 3.0 years ago by haansi50
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Answer: A: Heteroplasmy detection program
... Another shameless plug: you could use mtDNA-Server http://mtdna-server.uibk.ac.at/ - it was designed just for this specific task - to determine heteroplasmy in mtDNA ngs data. It also performs a contamination check, based on haplotype / haplogroup checking. For local usage I can recommend LoFreq - ...
written 3.0 years ago by haansi50
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Comment: C: Retrieve All Population Frequency Data For A Snp In 1000Genomes Phase_1
... Hi Peixe! Thank you very much for this very interesting web-app!! Just gave it a try - unfortunately there's only data from 1000Genomes Pilot 1 not but not from 1000Genomes Phase 1. Otherwise a very cool and fast application! ...
written 6.6 years ago by haansi50
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Comment: C: Retrieve All Population Frequency Data For A Snp In 1000Genomes Phase_1
... Hi Zev! Thank you very much for your answer! Found this approach also in a previous question (http://www.biostars.org/p/6897/). Wasn't aware of the ftp file you mentioned though. I gave it a try, the query time was about 5 seconds (could live with it), but I need all informtions to frequencys as her ...
written 6.6 years ago by haansi50
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Retrieve All Population Frequency Data For A Snp In 1000Genomes Phase_1
... Hi all! Just found this entry: http://www.biostars.org/p/6699/ which is very close to what i need. Similar to Krisr I would like to retrieve all population frequency data available from 1000Genomes phase 1 for a SNP, if possible via SQL. Ensembls Biomart provides minor allele information for the ...
1000genomes variation bioperl snp written 6.6 years ago by haansi50 • updated 6.6 years ago by Peixe580
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Answer: A: How To Get The Mutation List For Mtdna Complete Sequence Submitted In Genbank?
... Although this is an older question - maybe this can still be useful: you can use the GenBank mtDNA Sequence Checker on Ian Logans Website: http://www.ianlogan.co.uk/checker/genbank.htm or use Web-Tools such as mitomaster: http://mitomaster.research.chop.edu/MITOMASTER or MitoTool http://www.mitotoo ...
written 6.6 years ago by haansi50

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Popular Question 5.1 years ago, created a question with more than 1,000 views. For Retrieve All Population Frequency Data For A Snp In 1000Genomes Phase_1

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