User: kristina.mahan

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Posts by kristina.mahan

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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 4 days ago by kristina.mahan20
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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 4 days ago by kristina.mahan20
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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 5 days ago by kristina.mahan20
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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 5 days ago by kristina.mahan20
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Comment: C: Debugging a sed script to extract values from rows in .txt file
... The original vcf has 8 columns and in the 8th column- "info" is has this string all together in same column (multiple rows): AC=1;AF=0.500;AN=2;BaseQRankSum=-2.790;DP=300;ExcessHet=3.0103;FS=3.218;MLEAC=1;MLEAF=0.500;MQ=55.83;MQRankSum=-11.767;QD=15.75;ReadPosRankSum=2.193;SOR=0.890 AC=1;AF ...
written 5 days ago by kristina.mahan20
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Comment: C: Debugging a sed script to extract values from rows in .txt file
... I tried to extract values for ReadPosRankSum using same sed command: cut -f 8 | \ sed 's/^.*;ReadPosRankSum=\(\-\{0,1\}[0-9]\{1,\}.[0-9]*\);.*$/\1/' > ReadPosRankSum.txt Here are a few lines of the .txt file showing it extracted some but not all of the value even though ReadPosRankSum i ...
written 5 days ago by kristina.mahan20
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Debugging a sed script to extract values from rows in .txt file
... I am trying to extract out all the values for a specific quality filter MQRankSum. Someone has given a sed script showing how they did it. Here is one row of my .txt file all located in column 8: AC=1;AF=0.500;AN=2;BaseQRankSum=-0.181;DP=350;ExcessHet=3.0103;FS=134.905;MLEAC=1;MLEAF=0.500;MQ=5 ...
sed unix regex written 5 days ago by kristina.mahan20
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Plot line graph when counts are not automatically given
... I want to plot Depth of Coverage values in R. I've extracted all the Coverage values from my VCF and want to plot it. The x-axis would be Depth and the y-axis would be counts. I don't have the counts specified I just have a .txt file with a column of values. In R: library(ggplot2) filenam ...
vcf R ggplot2 depth written 5 days ago by kristina.mahan20 • updated 5 days ago by zx87545.3k
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Comment: C: Spades Assembly stopping
... SPAdes 3.12.0. The assembly is actually running now. So I bet it will still say "Thanks for using Spades" when it's done. Thanks alot! ...
written 15 days ago by kristina.mahan20
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Comment: C: Spades Assembly stopping
... 23:03:07.547 178G / 178G INFO General (hammer_tools.cpp : 175) Processed batch 34 23:03:15.307 178G / 178G INFO General (hammer_tools.cpp : 185) Written batch 34 23:03:25.251 166G / 178G INFO General (hammer_ ...
written 16 days ago by kristina.mahan20

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