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User: kristina.mahan

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Posts by kristina.mahan

<prev • 28 results • page 1 of 3 • next >
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Comment: C: filtering the somatic variants
... Check this: http://mbontrager.org/blog/2016/08/17/Variant-Exploration ...
written 7 weeks ago by kristina.mahan • 20
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Comment: C: Visualize Variant Density using Python
... callset.keys() [u'calldata', u'samples', u'variants'] ...
written 7 weeks ago by kristina.mahan • 20
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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 7 weeks ago by kristina.mahan • 20
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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 7 weeks ago by kristina.mahan • 20
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Comment: C: How to annotate chloroplast genome
... I guess what I want to do is take my mapped reads with annotations and visualize in geneious or IGV. ...
written 7 weeks ago by kristina.mahan • 20
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How to annotate chloroplast genome
... I mapped sequencing reads to a published chloroplast genome. A annotation file is available for the reference chloroplast genome. How can I annotate the bam file I created? ...
.gff annotation bam written 7 weeks ago by kristina.mahan • 20 • updated 7 weeks ago by goodez • 420
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Comment: C: Plot line graph when counts are not automatically given
... 'data.frame': 725952 obs. of 1 variable: $ V1: num 478 569 568 620 609 545 242 240 229 346 ... ...
written 9 weeks ago by kristina.mahan • 20
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Comment: C: Plot line graph when counts are not automatically given
... When I do that I get this error: Error: StatBin requires a continuous x variable: the x variable is discrete. Perhaps you want stat="count"? ...
written 9 weeks ago by kristina.mahan • 20
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Comment: C: Debugging a sed script to extract values from rows in .txt file
... can you interpret the sed command you are suggesting so that I can understand it? Please :) ...
written 9 weeks ago by kristina.mahan • 20
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Comment: C: Debugging a sed script to extract values from rows in .txt file
... here is a few rows of the original vcf showing that the info column as the 8th column: unitig_2993_pilon 30545 . G T 2880.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.181;DP=350;ExcessHet=3.0103;FS=134.905;MLEAC=1;MLEAF=0.500;MQ=50.03;MQRankSum=-7.801;QD=8.35;ReadPosRankSum=-1.213;SOR=4.021 GT:AD:DP ...
written 9 weeks ago by kristina.mahan • 20

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