User: fbrundu

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fbrundu260
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Posts by fbrundu

<prev • 60 results • page 1 of 6 • next >
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Answer: A: Is cnvkit coverage output split into non-overlapping segments?
... There are no overlaps (at least not in my results), you can check yours with: for file in $( find . -name "*.sort.targetcoverage.cnn" ) do tail +2 $file | sort -k1,1 -k2n,2 | \ awk 'BEGIN{ chr=0 } { if($1==chr) { if($2 ...
written 7 months ago by fbrundu260
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Is cnvkit coverage output split into non-overlapping segments?
... I am trying to compute breadth of coverage for exome data using cnvkit coverage command. The output is in the form chromosome start end gene depth log2 1 12098 12258 LOC102725121,DDX11L1 396.431 8.63093 1 12553 12721 LOC102725121,DDX11L1 402.667 8.65344 1 13331 13701 LOC102725121,D ...
exome cnvkit coverage written 7 months ago by fbrundu260 • updated 6 months ago by Eric T.2.1k
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Comment: C: Compute mean depth coverage for exome data with paired end, overlapping, feature
... Thanks.. `bedtools merge` is exactly what I was looking for! ...
written 7 months ago by fbrundu260
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Comment: C: Compute mean depth coverage for exome data with paired end, overlapping, feature
... Thanks Kevin. My doubt is, to get the average coverage, since I have overlapping regions, it is necessary to get the per-base read depth, right? ...
written 7 months ago by fbrundu260
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Compute mean depth coverage for exome data with paired end, overlapping, features
... I am trying to get the mean depth coverage for bam files with bedtools. So far I've been using the command: ```bedtools coverage -hist -abam bamfile.bam -b targets_exome.bed > bamfile.bam.hist.all.txt``` But I find myself with a result similar to: 1 9998 10030 HWI-H217:64:C48Y8ACXX:4:1110 ...
exome bam coverage depth written 7 months ago by fbrundu260 • updated 7 months ago by Kevin Blighe19k
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TruSeq Exome Kit bed file old version
... I have to run an analysis using Whole Exome Sequencing (WXS) data prepared with the TruSeq Exome Kit (2012). I need the `.bed` file for the kit and I found it [here][1]. However, this file was posted on Nov. 16, 2015, while the kit used in my case is from 2012. I searched but I didn't find the bed ...
bedfile whole-exome-sequencing written 7 months ago by fbrundu260
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Comment: C: CNVkit calling strategies with matched-normal tumor
... Actually not, it's proprietary data. Thanks ...
written 7 months ago by fbrundu260
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Comment: C: CNVkit calling strategies with matched-normal tumor
... Yes, I'm using the batch command. I was thinking this was the best approach, too. ...
written 7 months ago by fbrundu260
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CNVkit calling strategies with matched-normal tumor
... I want to use cnvkit to call copy number alterations (CNAs) from Whole Exome Sequencing data (WES) of a specific tumor. I have a set of WES tumor samples, some of which also have the matched normal sample. My question is: would be more effective, to call CNAs for each tumor, the whole set of matche ...
cnvkit whole-exome copy-number-variation written 7 months ago by fbrundu260 • updated 7 months ago by Kevin Blighe19k
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Which data format for mRNA expression matrix is necessary to run pathway analysis with Paradigm?
... I am running Paradigm on a matrix of mRNA expression. I read Vaske, Charles J., et al. "Inference of patient-specific pathway activities from multi-dimensional cancer genomics data using PARADIGM." Bioinformatics 26.12 (2010): i237-i245. and also the help section in the web application. However it ...
pathway mrna gene-expression paradigm written 3.2 years ago by fbrundu260

Latest awards to fbrundu

Scholar 7 months ago, created an answer that has been accepted. For A: Is cnvkit coverage output split into non-overlapping segments?
Great Question 2.3 years ago, created a question with more than 5,000 views. For How to download a full matrix of gene expression of a TCGA dataset
Good Question 2.3 years ago, asked a question that was upvoted at least 5 times. For How To Check If Illumina Fastq Is Single Or Paired End With Minimal Sequence Id
Epic Question 2.3 years ago, created a question with more than 10,000 views. For How To Check If Illumina Fastq Is Single Or Paired End With Minimal Sequence Id
Popular Question 2.3 years ago, created a question with more than 1,000 views. For How To Find Gene - Probe Mapping For A Specific Affymetrix Platform
Popular Question 2.3 years ago, created a question with more than 1,000 views. For For Which Reason Is Useful To Do Gene Wise Normalization In Microarray Matrices?
Student 2.3 years ago, asked a question with at least 3 up-votes. For How to download a full matrix of gene expression of a TCGA dataset
Student 2.3 years ago, asked a question with at least 3 up-votes. For How To Check If Illumina Fastq Is Single Or Paired End With Minimal Sequence Id
Great Question 2.9 years ago, created a question with more than 5,000 views. For How To Check If Illumina Fastq Is Single Or Paired End With Minimal Sequence Id
Popular Question 2.9 years ago, created a question with more than 1,000 views. For How to download a full matrix of gene expression of a TCGA dataset
Popular Question 2.9 years ago, created a question with more than 1,000 views. For How To Merge Two Microarrays Datasets?
Popular Question 2.9 years ago, created a question with more than 1,000 views. For Warning Using Dwd Matlab Package And Results Matrix Not Fully Non Negative
Popular Question 2.9 years ago, created a question with more than 1,000 views. For How To Find Gene - Probe Mapping For A Specific Affymetrix Platform
Popular Question 2.9 years ago, created a question with more than 1,000 views. For How To Get Cdf For A Specific Cel
Popular Question 3.1 years ago, created a question with more than 1,000 views. For How To Define Batch And Covariate To Remove Batch Effects With Combat.R
Popular Question 3.1 years ago, created a question with more than 1,000 views. For In Which Order Use Normalization And Batch Effects Removal?
Popular Question 3.1 years ago, created a question with more than 1,000 views. For How to download a full matrix of gene expression of a TCGA dataset

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