User: Nicola Casiraghi

Reputation:
420
Status:
Trusted
Location:
Trento, IT
Website:
https://www.linkedin.c...
Scholar ID:
Google Scholar Page
Last seen:
an hour ago
Joined:
3 years, 5 months ago
Email:
c**************@gmail.com

about me

Posts by Nicola Casiraghi

<prev • 69 results • page 1 of 7 • next >
1
vote
0
answers
299
views
0
answers
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 5 months ago by Nicola Casiraghi420 • updated 5 months ago by genomax32k
0
votes
1
answer
477
views
1
answers
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 14 months ago by Nicola Casiraghi420
2
votes
1
answer
477
views
1
answers
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 14 months ago by Nicola Casiraghi420
0
votes
0
answers
421
views
0
answers
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 15 months ago by Nicola Casiraghi420
0
votes
1
answer
533
views
1
answers
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 15 months ago by Nicola Casiraghi420
1
vote
1
answer
414
views
1
answers
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 15 months ago by Nicola Casiraghi420
0
votes
1
answer
1.1k
views
1
answers
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 15 months ago by Nicola Casiraghi420
0
votes
2
answers
656
views
2
answers
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 15 months ago by Nicola Casiraghi420
4
votes
67
answers
25k
views
67
answers
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 16 months ago by Nicola Casiraghi420
5
votes
2
answers
434
views
2
answers
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 17 months ago by Nicola Casiraghi420 • updated 17 months ago by Jean-Karim Heriche12k

Latest awards to Nicola Casiraghi

Great Question 9 weeks ago, created a question with more than 5,000 views. For problems in hg19 and b37 compatibility
Popular Question 3 months ago, created a question with more than 1,000 views. For From genomic coordinate to Reference base
Popular Question 8 months ago, created a question with more than 1,000 views. For Hiseq Analysis Software Alignment
Popular Question 11 months ago, created a question with more than 1,000 views. For BICseq R package problem
Popular Question 12 months ago, created a question with more than 1,000 views. For Hiseq Analysis Software Alignment
Scholar 14 months ago, created an answer that has been accepted. For A: How to know a program I use is parallelizable?
Supporter 15 months ago, voted at least 25 times.
Teacher 15 months ago, created an answer with at least 3 up-votes. For A: Options for generating proportional Venn Diagram of 4 sets
Scholar 17 months ago, created an answer that has been accepted. For A: How to know a program I use is parallelizable?
Teacher 17 months ago, created an answer with at least 3 up-votes. For A: Options for generating proportional Venn Diagram of 4 sets
Popular Question 22 months ago, created a question with more than 1,000 views. For Hiseq Analysis Software Alignment
Popular Question 22 months ago, created a question with more than 1,000 views. For BICseq R package problem
Scholar 2.2 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 2.2 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 2.2 years ago, created an answer with at least 3 up-votes. For A: Options for generating proportional Venn Diagram of 4 sets
Teacher 2.2 years ago, created an answer with at least 3 up-votes. For A: Options for generating proportional Venn Diagram of 4 sets
Popular Question 2.4 years ago, created a question with more than 1,000 views. For problems in hg19 and b37 compatibility

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1374 users visited in the last hour