User: bdelolmo

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bdelolmo10
Reputation:
10
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New User
Location:
Barcelona
Last seen:
7 months, 1 week ago
Joined:
4 years, 4 months ago
Email:
b*******@gencardio.com

Posts by bdelolmo

<prev • 9 results • page 1 of 1 • next >
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faidx implementation with C++
... Hello, I am learning C++, and after learning STL I would like to do my own implementation of faidx to perform sequence extraction from a genome. I know there are nice APIs out there (seqAns, etc) but I want to understand the principles behind it. I have tried to understand the faidx implementati ...
fasta indexing c++ written 2.8 years ago by bdelolmo10 • updated 2.8 years ago by Matt Shirley9.3k
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Answer: A: CNV tool for small sequences
... I would add split-read/paired-end callers for increased sensitivity and breakpoint resolution (e.g Delly, Lumpy.,.). [Here you can find a list of available software for SV detection][1] [1]: https://omictools.com/search?q=structural%20variation ...
written 2.9 years ago by bdelolmo10
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Wessim and exome read simulation
... Hello, I am trying to do some exome-seq simulations with Wessim but without success. I can run the command without warnings, but when manually inspecting the reads with IGV I see them accumulated on the start and end coordinates for every targeted region (pic attached). https://ibb.co/f78drQ ![We ...
software error exome sequencing written 3.1 years ago by bdelolmo10 • updated 3.1 years ago by Pierre Lindenbaum128k
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Full intronic deletions on a Whole-Exome Sequencing experiment
... Hello, I am interested in analyzing Structural Variation in a set of samples from a WES experiment. I have used Pindel and Delly, and surprisingly I have found weird breakpoints in some genes that indicate a full deletion of the intronic regions. Does anyone know if this is an artifact? I was thin ...
wes whole-exome sequencing cnv deletion written 3.3 years ago by bdelolmo10 • updated 3.3 years ago by trausch1.5k
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Answer: A: Graph in R: sort alpha-numerically X-axis
... @ddiez, Thanks for answering. My problem was that for example after chr1:17000-17000 being the last interval from that chromosome, it should follow chr2:xxx-yyy following an alphanumeric order, but I was getting chr10:xxx-yyy. By using factors I can handle this, as you say, so many thanks. ...
written 3.5 years ago by bdelolmo10
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Graph in R: sort alpha-numerically X-axis
... Hello, I am facing the problem to plot a typical CNV plot using R (and ggplot2), with ratios on the Y axis and the chromosome and position interval on the X-axis (e.g chr1:17000-17100) but I only get it sorted numerically by default. Do you know how could I do it? ...
R ggplot cnv written 3.5 years ago by bdelolmo10
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RSVSim cannot simulate duplications
... Hello, I am trying to simulate some SVs using RSVSim. I can simulate both deletions and insertions at the same time, but the problem comes when I want to introduce duplications. This is the code that I use: `sim = simulateSV(output='.', genome=genome, chrs = "chr12", ins = 150, sizeIns = sizein ...
software error genome simulation written 3.9 years ago by bdelolmo10 • updated 3.8 years ago by choosehappy10
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Answer: A: Rearrangement of genome - can I try a local denovo assembly
... If the reference genome is well stablished I would suggest you to try some SV algorithms that are available. Paired End Mapping (PEM) algorithms need explicitly paired-end reads. If you have single-end you can try read depth (RD) or split-read methods (SR). There is a wide variety, I give you some ...
written 4.1 years ago by bdelolmo10
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DNAcopy for targeted sequencing
... Hello, I am trying DNAcopy for a gene panel, as expected, it merges the consecutive exons that have similar logratios. The problem comes when an entire gene has signals of a CNV. In that case DNAcopy finds the start of the CNV, but it also reports the first coordinate of the next gene as abnorma ...
dnacopy exome gene panel cnv written 4.1 years ago by bdelolmo10 • updated 4.1 years ago by Eric T.2.6k

Latest awards to bdelolmo

Popular Question 10 months ago, created a question with more than 1,000 views. For DNAcopy for targeted sequencing
Popular Question 2.5 years ago, created a question with more than 1,000 views. For Full intronic deletions on a Whole-Exome Sequencing experiment
Popular Question 2.5 years ago, created a question with more than 1,000 views. For DNAcopy for targeted sequencing

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