User: Nicola Casiraghi

Reputation:
440
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Location:
Trento, IT
Website:
https://www.linkedin.c...
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Last seen:
1 month ago
Joined:
4 years, 7 months ago
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c**************@gmail.com

about me

Posts by Nicola Casiraghi

<prev • 69 results • page 1 of 7 • next >
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Job: A postdoctoral position is available at CIBIO, University of Trento, Trento, Italy
... Location: CIBIO - University of Trento Advisor: Francesca Demichelis, http://demichelislab.unitn.it The succesfull candidate will design and implement strategies to analyse and integrate genomics, transcriptomics and epigenetics data. The study leverages access to data generated with a range o ...
genomics epigenetics job transcriptomics written 19 months ago by Nicola Casiraghi440 • updated 19 months ago by genomax57k
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Comment: C: Number of SNPs by target sequencing
... Correct, or refer to the [ClinVar][1] dataset from NCBI. [1]: ftp://ftp.ncbi.nlm.nih.gov/pub/clinvar/ ...
written 2.4 years ago by Nicola Casiraghi440
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Answer: A: Number of SNPs by target sequencing
... First, you should retrieve the BED file with targeted regions for each panel: for example for panel TruSight One Sequencing Panel Kits you can find the link to BED file [Access the gene list and other product files »][1] in section *Product Configurations*. The BED file for this panel is named [TruS ...
written 2.4 years ago by Nicola Casiraghi440
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Comment: C: How to extract only probes that exist on 2 different platform?
... Do you have a file for each platform reporting the genomic coordinates of the probes? ...
written 2.4 years ago by Nicola Casiraghi440
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Answer: A: R - Count number of Samples with mutation per gene
... you can apply the function [`table()`][1] for each row in your VCF: > GENE1 = c(1,2,2,2,2,0,0,1,1,1) > table(GENE1) GENE1 0 1 2 2 4 4 thus the result is a vector with a counter for each genotype found in the considered gene. [1]: http://www.inside-r.org/r-doc/base/t ...
written 2.4 years ago by Nicola Casiraghi440
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Comment: C: compute count of position coverage with bedtools
... You could use R: bed = read.delim(exons.bed,as.is=T) bp_covered = sum(bed[,3]-bed[,2]) ...
written 2.4 years ago by Nicola Casiraghi440
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Answer: A: Plotting Coverage in R
... Not sure if I got the point. By the way in R [barplot][1](your_coverage_data_array,horiz=T) will output an horizontal barplot with your coverage data. [1]: https://stat.ethz.ch/R-manual/R-devel/library/graphics/html/barplot.html ...
written 2.4 years ago by Nicola Casiraghi440
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Comment: C: Best method to call SNPs/genotype many bam files from only a defined list of var
... I think that [GATK Haplotypecaller][1] using flag --dbsnp your_25000_SNPs.vcf should answer your question. [1]: https://www.broadinstitute.org/gatk/guide/tooldocs/org_broadinstitute_gatk_tools_walkers_haplotypecaller_HaplotypeCaller.php ...
written 2.5 years ago by Nicola Casiraghi440
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Answer: A: What Are The Most Common Stupid Mistakes In Bioinformatics?
... I spent hours to implement R parallel script to fully exploit 64 cores and 250 GB RAM of the server lab. Thus, really proud of myself, I run it on my 4 cores and 8 GB RAM desktop pc. Boom. ...
written 2.5 years ago by Nicola Casiraghi440
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manage huge arrays in R
... Hi all, working in R, I need to merge **24 big arrays** (on average **2.5 millions of points** each array and stored as RData) in order to compute overall statistics as mean, median and percentiles. Uploading all into memory is not feasible, thus I was wondering if you can suggest me some strategy t ...
R ff memory usage written 2.6 years ago by Nicola Casiraghi440 • updated 2.6 years ago by Jean-Karim Heriche16k

Latest awards to Nicola Casiraghi

Great Question 16 months ago, created a question with more than 5,000 views. For problems in hg19 and b37 compatibility
Popular Question 17 months ago, created a question with more than 1,000 views. For From genomic coordinate to Reference base
Popular Question 22 months ago, created a question with more than 1,000 views. For Hiseq Analysis Software Alignment
Popular Question 2.1 years ago, created a question with more than 1,000 views. For BICseq R package problem
Popular Question 2.2 years ago, created a question with more than 1,000 views. For Hiseq Analysis Software Alignment
Scholar 2.4 years ago, created an answer that has been accepted. For A: How to know a program I use is parallelizable?
Supporter 2.4 years ago, voted at least 25 times.
Teacher 2.4 years ago, created an answer with at least 3 up-votes. For A: Options for generating proportional Venn Diagram of 4 sets
Scholar 2.6 years ago, created an answer that has been accepted. For A: How to know a program I use is parallelizable?
Teacher 2.6 years ago, created an answer with at least 3 up-votes. For A: Options for generating proportional Venn Diagram of 4 sets
Popular Question 3.0 years ago, created a question with more than 1,000 views. For Hiseq Analysis Software Alignment
Popular Question 3.0 years ago, created a question with more than 1,000 views. For BICseq R package problem
Scholar 3.4 years ago, created an answer that has been accepted. For A: Make 2 boxplot from a data frame by plotting values in 1 row with different col
Scholar 3.4 years ago, created an answer that has been accepted. For A: Make 2 boxplot from a data frame by plotting values in 1 row with different col
Teacher 3.4 years ago, created an answer with at least 3 up-votes. For A: Options for generating proportional Venn Diagram of 4 sets
Teacher 3.4 years ago, created an answer with at least 3 up-votes. For A: Options for generating proportional Venn Diagram of 4 sets
Popular Question 3.6 years ago, created a question with more than 1,000 views. For problems in hg19 and b37 compatibility

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