User: user31888

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user3188880
Reputation:
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United States
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11 months, 3 weeks ago
Joined:
4 years, 9 months ago
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Posts by user31888

<prev • 85 results • page 1 of 9 • next >
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Comment: C: Copy Number Analysis on single file
... Good idea. I will give qPCR a try. Thanks ! ...
written 11 months ago by user3188880
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Comment: C: Copy Number Analysis on single file
... Alternatively, I need to calculate the approximative copy number (and exon involved) of a specific gene. Would it be possible to do it "manually" from a BAM or VCF file? ...
written 12 months ago by user3188880
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Comment: C: Issues installing bcftools with GNU Scientific Library
... Yes, I tried installing the GNU Scientific Library, then bcftools with conda. Both installations worked, but the GSL is not integrated/linked and thus I cannot get `polysomy`. ...
written 12 months ago by user3188880
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Issues installing bcftools with GNU Scientific Library
... I am trying to compile the latest `bcftools` (version 1.9) with the GNU Scientific Library, in order to be able to use the `polysomy` algorithm. I'm not sudo on the shared system, so I installed `zlib-1.2.11` in my home directory. Then in the bcftools directory I tried: ./configure --enable-l ...
zlib bcftools written 12 months ago by user3188880 • updated 12 months ago by ATpoint36k
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Comment: C: Copy Number Analysis on single file
... I also decreased the following parameters and still get the same error: minExpectedGC=0 minimalSubclonePresence=0 readCountThreshold=0 window=1 #(window=0 does not work) ...
written 12 months ago by user3188880
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Comment: C: Copy Number Analysis on single file
... It is about 10e6 bp. ...
written 12 months ago by user3188880
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Comment: C: Copy Number Analysis on single file
... Thanks Kevin ! The program generates the `sample.cnp` and `GC_profile.cnp` files, but then stops with the following error: Error: zero reads in windows with the GC-content around 0.35 with interval 0.01, will try again with 0.04 Error: zero reads in windows with the GC-content around 0.35 w ...
written 12 months ago by user3188880
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Comment: C: Copy Number Analysis on single file
... It is target sequencing. ...
written 12 months ago by user3188880
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Comment: C: Copy Number Analysis on single file
... `bcftools cnv` does not seem to work since we need to have 2 samples to compute LRR (Log R Ratio). ...
written 12 months ago by user3188880
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Comment: C: Copy Number Analysis on single file
... It seems that `bcftools cnv` could sort me out. I need to add to my vcf, the B-allele frequency (I can compute it from the AD field), and the LRR (don't know what it is yet), ...
written 12 months ago by user3188880

Latest awards to user31888

Popular Question 14 months ago, created a question with more than 1,000 views. For GATK DepthOfCoverage: 'total coverage' and 'mean coverage' meaning
Popular Question 19 months ago, created a question with more than 1,000 views. For bam-readcount installation problem: Linking CXX executable
Popular Question 19 months ago, created a question with more than 1,000 views. For bam-readcount installation problem: Linking CXX executable
Popular Question 2.1 years ago, created a question with more than 1,000 views. For bam-readcount installation problem: Linking CXX executable
Popular Question 2.1 years ago, created a question with more than 1,000 views. For GATK DepthOfCoverage: 'total coverage' and 'mean coverage' meaning
Popular Question 2.2 years ago, created a question with more than 1,000 views. For bam-readcount installation problem: Linking CXX executable
Popular Question 2.2 years ago, created a question with more than 1,000 views. For GATK DepthOfCoverage: 'total coverage' and 'mean coverage' meaning
Popular Question 2.8 years ago, created a question with more than 1,000 views. For bam-readcount installation problem: Linking CXX executable
Popular Question 2.8 years ago, created a question with more than 1,000 views. For GATK DepthOfCoverage: 'total coverage' and 'mean coverage' meaning
Popular Question 2.8 years ago, created a question with more than 1,000 views. For GAGE pathway analysis (R/Bioconductor): summarizeOverlaps error
Popular Question 2.8 years ago, created a question with more than 1,000 views. For Doc/tutorial UCSC MySQL
Popular Question 3.4 years ago, created a question with more than 1,000 views. For GAGE pathway analysis (R/Bioconductor): summarizeOverlaps error

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