User: kristina.mahan

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Posts by kristina.mahan

<prev • 34 results • page 1 of 4 • next >
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Comment: A: Error when trying to run IGV on server
... (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.mahan50
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Error when trying to run IGV on server
... 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 ...
igv written 9 weeks ago by kristina.mahan50
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Plotting Allele Frequencies
... 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 ...
ad causative variant variant analysis af dp written 3 months ago by kristina.mahan50 • updated 3 months ago by h.mon28k
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Comment: C: VCF file analysis to find genome wide association
... okay I will do that! ...
written 3 months ago by kristina.mahan50
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Comment: C: VCF file analysis to find genome wide association
... 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.mahan50
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Comment: C: VCF file analysis to find genome wide association
... 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.mahan50
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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.mahan50
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Comment: C: Visualize Variant Density using Python
... callset.keys() [u'calldata', u'samples', u'variants'] ...
written 13 months ago by kristina.mahan50
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Comment: C: How to annotate chloroplast genome
... 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.mahan50
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Visualize Variant Density using Python
... 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 ...
variant density python written 13 months ago by kristina.mahan50

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