User: kristina.mahan
kristina.mahan • 50
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Posts by kristina.mahan
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... (igv) [kmmahan@blogin4 analysis]$ java -version
openjdk version "1.7.0_91"
OpenJDK Runtime Environment (Zulu 7.12.0.3-linux64) (build 1.7.0_91-b15)
OpenJDK 64-Bit Server VM (Zulu 7.12.0.3-linux64) (build 24.91-b15, mixed mode)
So it is using JDK instead of JVM? ...
written 9 weeks ago by
kristina.mahan • 50
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... I want to use IGV on a server so I don't have to download bam files to my local machine. I used conda to install igvtools. When I type igvtools in the command line I get this error:
Using system JDK.
Unrecognized option: --module-path=/home/kmmahan/miniconda3/envs/igv/share/igvtools-2.5.3-0/lib
Err ...
written 9 weeks ago by
kristina.mahan • 50
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... I have UV mutagenized microorganisms and screened for improved phenotypes. Now I want to identify the causative variants. I've sequenced (200x coverage) a cultivar (mixed population with improved phenotype) and have vcfs with thousands of variants. I was wanting to do GWAS and make some Manhattan Pl ...
written 3 months ago by
kristina.mahan • 50
• updated
3 months ago by
h.mon ♦ 28k
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... okay I will do that! ...
written 3 months ago by
kristina.mahan • 50
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... Illumina DNA sequencing - providing about 200x coverage. Hoping that since this is a mixed population that was selected for a specific improvement in phenotype- that the causative variant would be more dominant in the population. I have VCF files that have thousands of variants that I would like to ...
written 3 months ago by
kristina.mahan • 50
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... Kevin- if you sequenced a mixed population of bacteria that was selected for an improved phenotype (each sequencing read representing a separate individual)- is it possible to identify the significant variant associated with the phenotype? Is that what was done here? ...
written 4 months ago by
kristina.mahan • 50
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Comment:
C: filtering the somatic variants
... Check this: http://mbontrager.org/blog/2016/08/17/Variant-Exploration ...
written 13 months ago by
kristina.mahan • 50
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... callset.keys()
[u'calldata', u'samples', u'variants'] ...
written 13 months ago by
kristina.mahan • 50
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... I have several chloroplast genomes I want to compare. Mine will match more closely with one of the other two. I'm not trying to look at coverage. So what I have now is reads mapped onto each reference (.bam files). and now I want to compare all of them together. Will those tools allow that? I wanted ...
written 13 months ago by
kristina.mahan • 50
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... I found these instructions on visualizing variant density using python: http://alimanfoo.github.io/2016/06/10/scikit-allel-tour.html
Step 1 is to open HDF5 callset:
callset_fn = 'data/2016-06-10/ag1000g.phase1.ar3.h5'
callset = h5py.File(callset_fn, mode='r')
callset
Step 2 is to pick ...
written 13 months ago by
kristina.mahan • 50
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