User: Andy Lee

gravatar for Andy Lee
Andy Lee10
Reputation:
10
Status:
New User
Location:
Last seen:
1 year, 3 months ago
Joined:
2 years, 3 months ago
Email:
j******@umich.edu

Posts by Andy Lee

<prev • 6 results • page 1 of 1 • next >
6
votes
2
answers
894
views
5 follow
2
answers
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 16 months ago by Andy Lee10 • updated 16 months ago by ATpoint26k
2
votes
1
answer
588
views
1
answer
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 18 months ago by Andy Lee10 • updated 18 months ago by Eric T.2.5k
0
votes
0
answers
998
views
0
answers
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 19 months ago by Andy Lee10
0
votes
1
answer
554
views
1
answers
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 21 months ago by Andy Lee10
0
votes
1
answer
554
views
1
answer
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 21 months ago by Andy Lee10
0
votes
0
answers
1.0k
views
0
answers
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 2.1 years ago by Andy Lee10 • updated 11 months ago by Yijun Tian20

Latest awards to Andy Lee

No awards yet. Soon to come :-)

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1112 users visited in the last hour