User: user31888

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user3188880
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United States
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5 months, 4 weeks 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 6 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 6 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 6 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 6 months ago by user3188880 • updated 6 months ago by ATpoint29k
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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 6 months ago by user3188880
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Comment: C: Copy Number Analysis on single file
... It is about 10e6 bp. ...
written 6 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 6 months ago by user3188880
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Comment: C: Copy Number Analysis on single file
... It is target sequencing. ...
written 6 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 6 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 6 months ago by user3188880

Latest awards to user31888

Popular Question 8 months ago, created a question with more than 1,000 views. For GATK DepthOfCoverage: 'total coverage' and 'mean coverage' meaning
Popular Question 13 months ago, created a question with more than 1,000 views. For bam-readcount installation problem: Linking CXX executable
Popular Question 13 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 19 months ago, created a question with more than 1,000 views. For GATK DepthOfCoverage: 'total coverage' and 'mean coverage' meaning
Popular Question 21 months ago, created a question with more than 1,000 views. For bam-readcount installation problem: Linking CXX executable
Popular Question 21 months ago, created a question with more than 1,000 views. For GATK DepthOfCoverage: 'total coverage' and 'mean coverage' meaning
Popular Question 2.4 years ago, created a question with more than 1,000 views. For bam-readcount installation problem: Linking CXX executable
Popular Question 2.4 years ago, created a question with more than 1,000 views. For GATK DepthOfCoverage: 'total coverage' and 'mean coverage' meaning
Popular Question 2.4 years ago, created a question with more than 1,000 views. For GAGE pathway analysis (R/Bioconductor): summarizeOverlaps error
Popular Question 2.4 years ago, created a question with more than 1,000 views. For Doc/tutorial UCSC MySQL
Popular Question 2.9 years ago, created a question with more than 1,000 views. For GAGE pathway analysis (R/Bioconductor): summarizeOverlaps error

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