User: ibphuangchen

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ibphuangchen10
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New User
Location:
United States
Last seen:
8 months, 4 weeks ago
Joined:
3 years, 4 months ago
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Posts by ibphuangchen

<prev • 5 results • page 1 of 1 • next >
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Comment: C: Using THETA2 from CNVkit: what king of vcf do you need?
... Does this command line: cnvkit.py export theta Sample_T.cns reference.cnn -v Sample_Paired.vcf currently support the VCF outputs from Mutect2 now? A unfiltered output VCF file from Mutect2 should also contain germline variants (as indicated by "germlink_risk" in the FILTER column. May be I' ...
written 13 months ago by ibphuangchen10
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Comment: C: CNVkit - how many normal samples do I need for the pooled normal reference?
... Hi Eric, Thanks for the prompt reply. My normal samples are indeed blood cells from the patients. I had been concerned that only using 10-20 instead of all the normal BAMs might not be able (i.e. not sufficient enough) to reflect all the normal samples in the cohort. I understand that this pooled ...
written 13 months ago by ibphuangchen10
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CNVkit - how many normal samples do I need for the pooled normal reference?
... Hi guys, I'm using CNVkit to process my WES data to get copy number alternation. I have 110 tumor samples, each of them has got a matched normal. CNVkit suggests to use pool normal for the normal reference. I was wondering do I need to plug in all these 110 normal .bam files for the normal referenc ...
genome cnvkit written 13 months ago by ibphuangchen10 • updated 13 months ago by Eric T.2.4k
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Answer: A: how to combine methylation information from different platform?
... Try this R package: MethyLiftOver https://www.ncbi.nlm.nih.gov/pubmed/27153617 ...
written 23 months ago by ibphuangchen10
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why cuffmerge need a fasta sequence as running parameter
... Hi there, -- I've got a question when I go through the tuxedo RNA-seq data processing, -- why cuffmerge need a fasta sequence as running parameter (i.e. "-s genome.fa") ? I would imagine that what cuffmerge does is to further assemble transcripts that have been "preliminarily assembled' by cufflin ...
assembly rna-seq cuffmerge written 3.4 years ago by ibphuangchen10

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