User: Andy Lee

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Andy Lee10
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2 years, 2 months ago
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3 years, 2 months ago
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j******@umich.edu

Posts by Andy Lee

<prev • 6 results • page 1 of 1 • next >
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Compute average score across multiple bed files
... I would like to compute the average score across multiple bed files (say from ChIP-seq) for a specific genomic region. Let's say I have the following three bed files and I wish to compute the average score for chr1:10-20 a.bed chr start end score chr1 10 20 3 b.bed chr start end sco ...
R chip-seq python bed written 2.4 years ago by Andy Lee10 • updated 2.4 years ago by ATpoint42k
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Using CNVkit to identify poor-quality normal samples
... **Problem** I am trying to run the analysis specified below: http://cnvkit.readthedocs.io/en/stable/tumor.html under "Next steps" > For the careful: Run batch with just the normal samples specified as > normal, yielding coverage .cnn files and a pooled reference. Inspect > the coverages ...
cnvkit written 2.5 years ago by Andy Lee10 • updated 2.5 years ago by Eric T.2.6k
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How do you run GISTIC2 with ExomeCNV outputs?
... I am using ExomeCNV to call copy numbers of some whole exome sequencing data (tumor and normal). I'd like to use GISTIC2.0 (standalone) to identify recurrent CNVs. The outputs of ExomeCNV are as follow: - chr - probe_start - probe_end - coverage - targeted.base - sequenced.base - copy.number - logR ...
gistic exomecnv copy number cnv written 2.6 years ago by Andy Lee10
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Answer: A: Trying to use Siphy to get pi scores for each position
... Never mind. I figured this out. It turns out the maf file needs to match the mod file. ...
written 2.8 years ago by Andy Lee10
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Trying to use Siphy to get pi scores for each position
... I am trying to use Siphy (Garber, M. et al, 2009), but am having some difficulties. I am trying to get the log-odds pi scores for each position in one of the hg18 chromosomes. I used the following command line but the intended output does not seem to be generated: java -jar bin/scaler_0.5.jar -tas ...
conservation broad siphy written 2.8 years ago by Andy Lee10
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TCGA PRAD Biochemical Recurrence Data Problem
... I downloaded the TCGA prostate adenocarcinoma clinical data from the following url: https://xenabrowser.net/datapages/?dataset=TCGA.PRAD.sampleMap/PRAD_clinicalMatrix&host=https://tcga.xenahubs.net In the clinicalMatrix file, the "biochemical_recurrence" field for the following sample ids ...
tcga xena browser data error prad written 3.1 years ago by Andy Lee10 • updated 23 months ago by Yijun Tian20

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