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Problems using cnvkit for ctDNA targeted sequencing

cnvkit ctdna results written 16 days ago by ingrid.schulman • 0 • updated 13 days ago by Eric T. • 1.8k

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Tool: MAGERI: a software tool for calling rare variants and detecting circulating tumor DNA from UMI-tagged high-throughput sequencing data

rare variant umi resequencing ctdna tool written 3 months ago by mikhail.shugay ♦ 3.2k

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339

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Job: Senior Bioinformatician Position at AnchorDx

ctdna next-gen methylation job somatic mutation written 4 months ago by weihong_xu • 30

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387

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Detecting variants at very low fractions from ctDNA

ctdna mutation variants written 9 months ago by CY • 30 • updated 9 months ago by Tonor • 400

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Recent Replies

C: RNA-Seq or Exome Seq for Clinical data analysis by WouterDeCoster ♦ 20k
So, to summarize, we have - fishy - odd - strange That's rather remarkable, isn't it?
C: RNA-Seq or Exome Seq for Clinical data analysis by Brian Bushnell ♦ 13k
I *thought* it was strange that I got +6 on a random answer that anyone could have given. In, li...
C: problem in loading systemPipeR and RNASeqGene packages in R 3.4.1 by nazaninhoseinkhan • 190
I forgot to say that I get the error message when I want to install "airway" package which is a p...
C: RNA-Seq or Exome Seq for Clinical data analysis by WouterDeCoster ♦ 20k
After my comment 2 upvotes on the question itself were removed. Odd.
C: problem in loading systemPipeR and RNASeqGene packages in R 3.4.1 by h.mon ♦ 8.0k
What is the output of `sessionInfo()`?
C: problem in loading systemPipeR and RNASeqGene packages in R 3.4.1 by nazaninhoseinkhan • 190
I am trying to run RNASeq analysis on R 3.4.1 in windows 7
C: problem in loading systemPipeR and RNASeqGene packages in R 3.4.1 by e.rempel • 250
What OS do you have?
A: How to create a design matrix for Cpg.annotate? by e.rempel • 250
I will provide a short answer here, but I would strongly recommend you to read more about statist...
C: Meerkat for identification of somatic structural variations for paired samples by Albert Shih • 0
Hi, I'm also trying to detect somatic SV from our WES data (paired sample too), and I also get em...
C: PhD in bioinformatics or biostatistics as a wet-lab scientist? by azeem839839 • 0
Sure I also moved from M.Phil microbiology to PhD bioinformatics. but remember it require great i...
A: Rename headers of multiple fasta files inside loop by Matt Shirley ♦ 7.7k
You can use `pyfaidx` to do this in one step: $ pip install pyfaidx $ faidx -x -e "lambd...
A: faidx implementation with C++ by Matt Shirley ♦ 7.7k
You already have some pretty good answers, but I wanted to point out that I've done a Python impl...

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