User: Luca Beltrame

gravatar for Luca Beltrame
Luca Beltrame220
Reputation:
220
Status:
Trusted
Location:
IRCCS Istituto di Ricerche Farmacologiche "Mario Negri", Milano, Italy
Last seen:
2 months, 1 week ago
Joined:
6 years, 10 months ago
Email:
l************@marionegri.it

Posts by Luca Beltrame

<prev • 38 results • page 1 of 4 • next >
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Generate coordinates of specific length between two BED features
... Hello, as part of creating a custom library capture kit, I want to expand an existing design, which is provided to me as a single BED file. The coordinates for the existing design are spaced from 50kbp to 300kbp each, and the features are around 100bp each. What I'd like to do is to: 1. Get the m ...
bedtools bed written 10 weeks ago by Luca Beltrame220
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Comment: C: Merge regions in a BED but only if they share the same value (copy number) in a
... From a quick look it seems to do already what I want, I'll experiment a bit with it. ...
written 6 months ago by Luca Beltrame220
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Merge regions in a BED but only if they share the same value (copy number) in a column
... I have a BED similar to this: 1 47554 1341771 2 1 1341771 16237999 2 1 29269871 29386071 1 Where the last numeric column is the copy number calculated by another program. Now, you may notice that the interrvals there (the first two lines) have the same ...
bedtools bedops copy number written 6 months ago by Luca Beltrame220 • updated 6 months ago by ATpoint36k
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Aggregate multiple VCFs into a single MAF or generate a multi-sample MAF from a multi-sample VCF
... **Note:** This is different from the many `vcf2maf` questions posted around Biostars. Like many others, I've been in need to generate a MAF file for use in downstream applications like `maftools` or `TRONCO`. My final goal is to obtain a multi-sample MAF file like the ones shipped by TCGA. Howev ...
maf file-formats conversion sequencing written 3.2 years ago by Luca Beltrame220 • updated 9 months ago by d33jch0
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Proper way to plot VCF files from structural variant callers
... Hello, I already made and annotated a number of VCF files with LUMPY and manta, and I'd like to find a way to properly view them: while I'm fine looking through them programmatically, it is useless for the biologists that will need to look at the data. Unfortunately, extensive Google searches haven ...
visualization circos sequencing written 4.3 years ago by Luca Beltrame220
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Comment: C: Targeted NGS: amplicon length vs read length
... We don't use the MiSeq software, everything is done off-instrument. ...
written 4.4 years ago by Luca Beltrame220
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Targeted NGS: amplicon length vs read length
... Hello, In our group we are about to design an amplicon-based targeted panel for NGS, and we're aiming at around 150 bp for mean amplicon sizes. The wet lab people came back to me asking to calculate the optimal number of samples to be loaded in the instrument (MiSeq). And this is where I have my qu ...
amplicon next-gen sequencing written 4.4 years ago by Luca Beltrame220 • updated 4.4 years ago by WouterDeCoster44k
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Comment: C: Quality Control Software For Targeted Sequencing?
... Looks interesting. Now all that's "left" is to find a way to convert Illumina's manifest format to Picard interval.... ...
written 6.6 years ago by Luca Beltrame220
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Quality Control Software For Targeted Sequencing?
... I'm mainly doing (amplicon-based) resequencing over small (50-100) number of genes with the Illumina technology. Aside from the normal metrics for quality control produced by Qualimap and FastQC, I'm wondering if there's something out there (aside TEQC, see below for while) that targets specifically ...
software ngs analysis sequencing written 6.6 years ago by Luca Beltrame220 • updated 6.6 years ago by brentp23k
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Comment: C: Build Phylogenetic Trees From Bam Files
... Thanks for the answer. I'm using retargeted sequencing on small number of targets (30 genes), so I'm assuming it won't be a big problem. When you mention a consensus sequence, you mean using stuff like pileup to generate it? ...
written 6.7 years ago by Luca Beltrame220

Latest awards to Luca Beltrame

Epic Question 3.1 years ago, created a question with more than 10,000 views. For Color Clustering Results Basing On Sample Classes In R
Popular Question 3.1 years ago, created a question with more than 1,000 views. For Proper way to plot VCF files from structural variant callers
Popular Question 3.1 years ago, created a question with more than 1,000 views. For How To Represent Two Different Indels At The Same Position In A Multisample Vcf?
Popular Question 3.1 years ago, created a question with more than 1,000 views. For Visualization Tools For Ngs Analysis Results, Suitable For Biologists
Student 3.1 years ago, asked a question with at least 3 up-votes. For Color Clustering Results Basing On Sample Classes In R
Popular Question 4.1 years ago, created a question with more than 1,000 views. For How To Interpret Dp Fields For Samples In Vcf Files?
Popular Question 4.1 years ago, created a question with more than 1,000 views. For How To Handle Reads Ending With Deletions In Gatk?
Popular Question 4.3 years ago, created a question with more than 1,000 views. For Convert Cds-Based Coordinate To Genomic Coordinates
Great Question 6.4 years ago, created a question with more than 5,000 views. For Color Clustering Results Basing On Sample Classes In R
Popular Question 6.4 years ago, created a question with more than 1,000 views. For How To Represent Two Different Indels At The Same Position In A Multisample Vcf?
Popular Question 6.4 years ago, created a question with more than 1,000 views. For Re-Annotating An Existing Gff File?
Popular Question 6.4 years ago, created a question with more than 1,000 views. For Build Phylogenetic Trees From Bam Files
Popular Question 6.4 years ago, created a question with more than 1,000 views. For Convert Cds-Based Coordinate To Genomic Coordinates
Popular Question 6.4 years ago, created a question with more than 1,000 views. For Finding The Number Of Reads Which Support A Variant In Vcf
Popular Question 6.4 years ago, created a question with more than 1,000 views. For How To Interpret Dp Fields For Samples In Vcf Files?
Popular Question 6.4 years ago, created a question with more than 1,000 views. For Targeted Sequencing - Calculating The Minimum Exon Coverage
Popular Question 6.4 years ago, created a question with more than 1,000 views. For Sequencing Depth And Mutation Frequency
Popular Question 6.4 years ago, created a question with more than 1,000 views. For Visualization Tools For Ngs Analysis Results, Suitable For Biologists
Popular Question 6.4 years ago, created a question with more than 1,000 views. For Color Clustering Results Basing On Sample Classes In R
Popular Question 6.4 years ago, created a question with more than 1,000 views. For Loess Normalization And Scale Issues
Student 6.4 years ago, asked a question with at least 3 up-votes. For Color Clustering Results Basing On Sample Classes In R

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