User: haansi

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haansi80
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Posts by haansi

<prev • 9 results • page 1 of 1 • next >
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Comment: C: How to check mitochondrial reference in GWAS data for HaploGrep analysis
... Hi! This sounds good, great to hear that. When you run haplogrep with the chip flag, the scores get better - it ignores the sites which are not investigated, the number of expected sites for a haplogroup gets limited to the one found on the microarray. This is not comparable to a complete-sequenci ...
written 21 hours ago by haansi80
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Comment: C: How to check mitochondrial reference in GWAS data for HaploGrep analysis
... Here are some more issues, pointing to a wrong reference as well: 750 G should be A 1438 G should be A 2706 G should be A 4769 G should be A 12705 A should be C 15326 G should be A 15487 T should be A ...
written 7 days ago by haansi80
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Comment: C: How to check mitochondrial reference in GWAS data for HaploGrep analysis
... That's correct Jeremy, HaploGrep does not perform a remapping/liftover here - so there's a strand issue - as both heavy and light-strands seem to be mixed in the mtSNPs on this MicroArray. Interestingly the Microarray is designed detecting purines (A/G) and only for transversions pyrimidines (C/T). ...
written 7 days ago by haansi80
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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 4.3 years ago by haansi80
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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 4.3 years ago by haansi80
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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 7.9 years ago by haansi80
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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 7.9 years ago by haansi80
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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 7.9 years ago by haansi80 • updated 7.9 years ago by Peixe600
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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 7.9 years ago by haansi80

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Popular Question 6.3 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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