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User: bernatgel

gravatar for bernatgel
bernatgel • 1.3k
Reputation:
1,290
Status:
Trusted
Location:
Barcelona, Spain
Twitter:
@bernatgel
Last seen:
17 hours ago
Joined:
4 years, 7 months ago
Email:
b********@gmail.com

about me

Posts by bernatgel

<prev • 76 results • page 1 of 8 • next >
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Comment: C: How to take reads from WGS fastq files in order to map it with Exome?
... You don't know which reads come from exonic regions until you map them. As far as I know your only option would be to first map them all and then, if needed, extract the "exome" regions. ...
written 5 weeks ago by bernatgel • 1.3k
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Answer: A: How to convert mutation position from gene coordinate to genome coordinate?
... You should be able to do it with VEP (https://www.ensembl.org/info/docs/tools/vep/index.html), but beware of possible ambiguities if you only have the gene name but not the specific transcript. You might assume it refers to the "canonical" (usually the longest) transcript, but that's not always the ...
written 5 weeks ago by bernatgel • 1.3k
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Answer: A: Need help with R script to edit x-axis of snp density plot
... I would recommend using a tool specific for plotting data on the genome such as [karyoploteR](http://bioconductor.org/packages/release/bioc/html/karyoploteR.html). With this kind of tools, you'll get all your chromosomes into scale for free. The code would be something like this (untested): li ...
written 6 weeks ago by bernatgel • 1.3k
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Answer: A: Simulated CNVs maintaining size
... Hi Crisr, You can use the R/Bioconductor package [regioneR](http://bioconductor.org/packages/regioneR/) for that. It has a function called `randomizeRegions` that will move around your CNV regions maintaing their size and taking care that the randomized regions do not overlap. If you set the `per.c ...
written 3 months ago by bernatgel • 1.3k
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Comment: C: Systems administrator of bioinformatics linux systems at IGTP, Barcelona
... Great. Sorry for the inconvenience and thanks for reporting the problem. ...
written 3 months ago by bernatgel • 1.3k
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Comment: C: Systems administrator of bioinformatics linux systems at IGTP, Barcelona
... Hi h.mon The IT people tell me that the site should be accessible now from Brazil. Could you check if you can access it? Thanks! ...
written 3 months ago by bernatgel • 1.3k
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Comment: C: Systems administrator of bioinformatics linux systems at IGTP, Barcelona
... Ok, that's weird. It would seem like our domain is not accessible (blocked?) from some internet providers... I'll pass this information to the IT people to see if they might have any idea of what's happening... Thanks for the report! ...
written 3 months ago by bernatgel • 1.3k
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Comment: C: Systems administrator of bioinformatics linux systems at IGTP, Barcelona
... Ok, thank. I'll contact out IT department to see what's happening. ...
written 3 months ago by bernatgel • 1.3k
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Comment: C: Systems administrator of bioinformatics linux systems at IGTP, Barcelona
... Oops, it should be accessible from anywhere in the world. Where are you connecting from? I've copied in the post the complete job offer, but it should be possible to get some info about the institute, etc... ...
written 3 months ago by bernatgel • 1.3k
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Job: Systems administrator of bioinformatics linux systems at IGTP, Barcelona
... We are seeking a **Linux systems administrator** who will be responsible for the management of [a scientific computing facility](http://www.germanstrias.org/technology-services/high-performance-computing/) that includes a 240 core cluster, several servers, workstations, 500 Tb raw disk storage and b ...
sysadmin joboffer job written 3 months ago by bernatgel • 1.3k

Latest awards to bernatgel

Good Answer 5 weeks ago, created an answer that was upvoted at least 5 times. For A: Permutation test with gene size and GC contents
Scholar 5 weeks ago, created an answer that has been accepted. For A: Testing for over-representation of chip-peaks
Popular Question 3 months ago, created a question with more than 1,000 views. For Scientific Programmer for Translational Bioinformatics of Hereditary Cancer at the IMPPC, Badalona, Barcelona, Spain
Good Answer 6 months ago, created an answer that was upvoted at least 5 times. For A: Permutation test with gene size and GC contents
Appreciated 6 months ago, created a post with more than 5 votes. For A: Viewing CNV read depth data along multiple chromosomes in a single plot via R
Appreciated 7 months ago, created a post with more than 5 votes. For A: Viewing CNV read depth data along multiple chromosomes in a single plot via R
Teacher 8 months ago, created an answer with at least 3 up-votes. For A: Сalculating fold-enrichment of ChIP-seq peaks intersecting with promoters (vs. g
Guru 11 months ago, received more than 100 upvotes.
Teacher 11 months ago, created an answer with at least 3 up-votes. For A: Сalculating fold-enrichment of ChIP-seq peaks intersecting with promoters (vs. g
Teacher 11 months ago, created an answer with at least 3 up-votes. For A: Сalculating fold-enrichment of ChIP-seq peaks intersecting with promoters (vs. g
Teacher 12 months ago, created an answer with at least 3 up-votes. For A: Сalculating fold-enrichment of ChIP-seq peaks intersecting with promoters (vs. g
Popular Question 14 months ago, created a question with more than 1,000 views. For Scientific Programmer for Translational Bioinformatics of Hereditary Cancer at the IMPPC, Badalona, Barcelona, Spain
Librarian 14 months ago, created a post with more than 10 bookmarks. For karyoploteR: uncircle your genomes
Scholar 16 months ago, created an answer that has been accepted. For A: Permutation test with gene size and GC contents
Prophet 16 months ago, created a post with more than 20 followers. For karyoploteR: uncircle your genomes
Voter 16 months ago, voted more than 100 times.
Teacher 16 months ago, created an answer with at least 3 up-votes. For A: Сalculating fold-enrichment of ChIP-seq peaks intersecting with promoters (vs. g
Appreciated 17 months ago, created a post with more than 5 votes. For A: Permutation test with gene size and GC contents
Scholar 17 months ago, created an answer that has been accepted. For A: Permutation test with gene size and GC contents
Teacher 17 months ago, created an answer with at least 3 up-votes. For A: Сalculating fold-enrichment of ChIP-seq peaks intersecting with promoters (vs. g
Teacher 17 months ago, created an answer with at least 3 up-votes. For A: Сalculating fold-enrichment of ChIP-seq peaks intersecting with promoters (vs. g
Appreciated 17 months ago, created a post with more than 5 votes. For A: Permutation test with gene size and GC contents
Teacher 17 months ago, created an answer with at least 3 up-votes. For A: Сalculating fold-enrichment of ChIP-seq peaks intersecting with promoters (vs. g
Teacher 20 months ago, created an answer with at least 3 up-votes. For A: Сalculating fold-enrichment of ChIP-seq peaks intersecting with promoters (vs. g
Scholar 20 months ago, created an answer that has been accepted. For A: Permutation test with gene size and GC contents
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