User: gaiusjaugustus

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Posts by gaiusjaugustus

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Comment: C: Patterns within groups with RNA-seq
... Yes, there is. I could divide it by certain covariates (survival, mutated genes, etc). But I want a more machine learning (clustering) sort of way that isn't limited by the covariates that I have available or think of. ...
written 19 months ago by gaiusjaugustus150
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Answer: A: detecting LoH in cancer genomes
... I've only worked with SNP data for LOH, but have suggested the following publications for allele-specific copy number analysis. Hopefully someone else can lend some experience with these or other methods. Good luck! 1. Shen, Ronglai and Seshan, Venkatraman, "FACETS: Allele-Specific Copy Number an ...
written 19 months ago by gaiusjaugustus150
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Patterns within groups with RNA-seq
... I have RNA-Seq data from patients with different stage cancer, and have done a differential expression analysis comparing stages to each other and stages to normal tissue. **However, what I'd like to do is look for expression signatures WITHIN one stage (late stage) of the cancer.** Any suggestion ...
chip-seq rna-seq written 19 months ago by gaiusjaugustus150 • updated 19 months ago by Hussain Ather940
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Public datasets (like Hapmap/1000 genomes) for DNA methylation?
... Hi, I am interested in doing some population-level studies using DNA methylation (from blood). Are there any public datasets that have this kind of information for many individuals from different ethnic backgrounds? As an example, something like 1000 Genomes or Hapmap, but using a DNA methylation ...
public methylation written 2.5 years ago by gaiusjaugustus150 • updated 2.5 years ago by Shicheng Guo7.6k
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CIMP markers in Infinium 450k Methylation Data (How To)
... I have methylation data for a group of patients done on the Infinium Methylation 450k platform. I want to look at the samples and determine if they are CIMP (CpG island methylator phenotype) positive or negative at the CIMP markers. I've run my data through the RnBeads pipeline in R, but am not su ...
R sequencing written 2.7 years ago by gaiusjaugustus150
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Comment: C: Samtools view does not recognize that I already have index file
... Thanks for the quick response. Is there an easy way to be sure that the BAM is sorted? I've started trying to sort and it's going to be a long while (files are 30+ GB each), so I'd rather not resort to re-sorting if I don't have to. Also, any way to tell how the index was generated? Again, index ...
written 2.8 years ago by gaiusjaugustus150
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Samtools view does not recognize that I already have index file
... Hello, I am trying to extract reads at 1 base pair from many bam files. Each bam file has a bai file with the same name+.bai in the same folder. When I run samtools view myfile.bam I get the output, but when I add coordinates such as samtools view myfile.bam "chr1:1-100000" I get the f ...
samtools written 2.8 years ago by gaiusjaugustus150 • updated 2.8 years ago by Brice Sarver2.6k
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TCGA VCF & MAF content
... I have downloaded all the VCF files for one cancer type from the TCGA. Upon annotation using Annovar, I notice that there are a lot more variants than I expected. So I have a few questions: 1. How should I process these downstream? I've already reduced the list based on those that passed. 2. I ...
vcf tcga written 3.2 years ago by gaiusjaugustus150 • updated 3.1 years ago by Cyriac Kandoth5.3k
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Comment: C: GATK Workflow for GATK in Cancer Samples
... Since this has been posted, this is the only additional information I've found. Be sure to read the comments, as there's some good info there! http://gatkforums.broadinstitute.org/wdl/discussion/5963/tumor-normal-paired-exome-sequencing-pipeline If there's an updated documentation, please post a l ...
written 3.3 years ago by gaiusjaugustus150
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Identify Population Specific SNPs from List of SNPs
... I have a list of SNPs (from an array, so a lot of them).  I want to pull out those that are informative for a particular population (e.g. YRI vs CEU from HapMap).  I usually use SPSmart to do this, but it can't handle so much information.  Is there any other way to do this?   Perhaps an R package ...
snp written 3.4 years ago by gaiusjaugustus150

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Great Question 6 months ago, created a question with more than 5,000 views. For Checking Version of Bioconductor
Popular Question 8 months ago, created a question with more than 1,000 views. For PennCNV run error (Can't exec detect_cnv.pl) Linux
Appreciated 9 months ago, created a post with more than 5 votes. For A: detecting LoH in cancer genomes
Good Answer 9 months ago, created an answer that was upvoted at least 5 times. For A: detecting LoH in cancer genomes
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Popular Question 2.4 years ago, created a question with more than 1,000 views. For GISTIC 2.0 Segment CN
Popular Question 3.2 years ago, created a question with more than 1,000 views. For GATK Workflow for GATK in Cancer Samples
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