User: Nicola Casiraghi

Reputation:
450
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Trusted
Location:
Germany, Heidelberg, DKFZ EMBL
Website:
https://github.com/nca...
Last seen:
9 hours ago
Joined:
5 years, 3 months ago
Email:
c**************@gmail.com

about me

Posts by Nicola Casiraghi

<prev • 71 results • page 1 of 8 • next >
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Comment: C: Problems wth cnvkit scatter for genes
... You can export the whole .cnr file as [SEG][1] tab-delimeted format and visualize it on [IGV][2] [1]: https://cnvkit.readthedocs.io/en/stable/fileformats.html?highlight=seg#seg [2]: https://software.broadinstitute.org/software/igv/ ...
written 10 weeks ago by Nicola Casiraghi450
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Get the read count per genomic bin for each 10x barcode (10x Genomics Single Cell Gene Expression protocol)
... Given the BAM output of Cell Ranger (that contains all reads for each barcodes-cells) I want to count reads mapped to genomic bins for each barcode. I combined answer from [How do I get the read counts for each barcode?][1] with option `-L` as in: samtools view -L bins.bed possorted_genome_bam ...
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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 2.3 years ago by Nicola Casiraghi450 • updated 2.3 years ago by genomax68k
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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 3.0 years ago by Nicola Casiraghi450
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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 3.0 years ago by Nicola Casiraghi450
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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 3.1 years ago by Nicola Casiraghi450
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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 3.1 years ago by Nicola Casiraghi450
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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 3.1 years ago by Nicola Casiraghi450
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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 3.1 years ago by Nicola Casiraghi450
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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 3.1 years ago by Nicola Casiraghi450

Latest awards to Nicola Casiraghi

Great Question 24 months ago, created a question with more than 5,000 views. For problems in hg19 and b37 compatibility
Popular Question 2.1 years ago, created a question with more than 1,000 views. For From genomic coordinate to Reference base
Popular Question 2.5 years ago, created a question with more than 1,000 views. For Hiseq Analysis Software Alignment
Popular Question 2.8 years ago, created a question with more than 1,000 views. For BICseq R package problem
Popular Question 2.9 years ago, created a question with more than 1,000 views. For Hiseq Analysis Software Alignment
Scholar 3.0 years ago, created an answer that has been accepted. For A: How to know a program I use is parallelizable?
Supporter 3.1 years ago, voted at least 25 times.
Teacher 3.1 years ago, created an answer with at least 3 up-votes. For A: Options for generating proportional Venn Diagram of 4 sets
Scholar 3.3 years ago, created an answer that has been accepted. For A: How to know a program I use is parallelizable?
Teacher 3.3 years ago, created an answer with at least 3 up-votes. For A: Options for generating proportional Venn Diagram of 4 sets
Popular Question 3.7 years ago, created a question with more than 1,000 views. For Hiseq Analysis Software Alignment
Popular Question 3.7 years ago, created a question with more than 1,000 views. For BICseq R package problem
Scholar 4.0 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 4.0 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 4.0 years ago, created an answer with at least 3 up-votes. For A: Options for generating proportional Venn Diagram of 4 sets
Teacher 4.0 years ago, created an answer with at least 3 up-votes. For A: Options for generating proportional Venn Diagram of 4 sets
Popular Question 4.3 years ago, created a question with more than 1,000 views. For problems in hg19 and b37 compatibility

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