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User: Carlos Borroto

gravatar for Carlos Borroto
Carlos Borroto • 1.5k
Reputation:
1,500
Status:
Trusted
Location:
Washington Metropolitan Area
Scholar ID:
Google Scholar Page
Last seen:
2 days, 3 hours ago
Joined:
6 years, 4 months ago
Email:
c*************@gmail.com

Masters in Bioinformatics with strong focus in computational genomics and gene expression analysis. Bioinformatics Analyst with over seven years of experience in international and domestic laboratory environments. Extensive experience in computational applications for laboratory data analyses.

Specialties:Bioinformatics, UNIX/Linux administration, Molecular Biology, Cell Biology.

Posts by Carlos Borroto

<prev • 80 results • page 1 of 8 • next >
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Answer: A: Difference Between Picards Mergebamalignment And Mergesamfiles
... Long detailed explanation from the [GATK forum][1]. > 3C. Restore altered data and apply & adjust meta information using MergeBamAlignment >MergeBamAlignment is a beast of a tool, so its introduction is longer. It does more than is implied by its name. Explaining these features requires ...
written 4 months ago by Carlos Borroto • 1.5k
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Comment: C: Introducing Clumpify: Create 30% Smaller, Faster Gzipped Fastq Files. And remov
... How do you think this will affect reads coming from two almost identical regions but for a few bases? For example SMN1/SMN2 have regions that are only differentiated by 1 base. Would `clumpify.sh` with the recommended allowed subs parameter remove non-duplicated reads for these two regions? --Carlo ...
written 7 months ago by Carlos Borroto • 1.5k
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Comment: C: Rsync and python for ftp.ncbi
... I think you are falling in the trap of the [XY problem][1]. Please tell us more about what you are trying to do. Even without the details of what you really want to do, I doubt you need to get python involved here, most probably rsync by itself can do it. [1]: http://meta.stackexchange.com/quest ...
written 15 months ago by Carlos Borroto • 1.5k
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Answer: A: How to calculate average coverage for all genes
... I recently found myself looking for the exact info. I too decided to go with bedtools. This is my final one liner assuming a pre-sorted bam file. bedtools coverage -sorted -d -g human_g1k_v37.genome -a genes.bed -b my_sorted.bam \ | sort -k4,4 \ | bedtools groupby -g 4 -c 8 -o mean ...
written 15 months ago by Carlos Borroto • 1.5k
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Answer: A: Human GRCh38 and dbSNP VCF and GATK
... You problem seems to be you are using a dbSNP VCF with GRCh37 coordinates. The FTP location Pierre links in his answer has a GRCh38 version that should solve your problem. However, you should know the current GATK version is not "alt" aware yet. While mappers like BWA are and can correctly map read ...
written 16 months ago by Carlos Borroto • 1.5k
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Answer: A: How do I get the lengths of different regions targeted by the Nextera expanded r
... You can use a GTF with annotated intervals for the categories you want. For example this [one][1] from Ensembl. Use something like unix grep to create files for the categories you are interested. Then use [bedtools intersect][2] to get the regions of your BED file overlapping with each category GTF ...
written 16 months ago by Carlos Borroto • 1.5k
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Comment: C: UMI for Exome Target Sequencing
... I'm currently looking for how to do phasing with targeted sequencing data. I wonder if that's the reason you are looking into adding UMI to an exome analysis. I'll be highly interested in seeing if there are any valid answers to your question. ...
written 17 months ago by Carlos Borroto • 1.5k
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Answer: A: ClinVar local install
... I recommend you use [Ensembl VEP][1]. Among other many relevant things to catalog a variant as damaging, you will get `CLIN_SIG` or ClinVar significance classifier. Using VEP's web interface for small jobs will work just fine. For larger jobs and for more customizable usage you can install it locall ...
written 17 months ago by Carlos Borroto • 1.5k
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Answer: A: Which Bioinformatic Friendly Pipeline Building Framework?
... The Broad recently [announced][1] their replacement for Queue, [Cromwell/WDL][2]. We just starting checking it out and it looks promising. When we did the initial search 2 years ago, we ended choosing Queue. It worked for us and it was nice to get free advanced scather-and-gather for GATK tools. How ...
written 17 months ago by Carlos Borroto • 1.5k
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Answer: A: How Successful are new Bioinformatics Software Companies?
... I don't think there is much value in selling bioinformatics software. Mostly for the reasons you described about the advantages of the open source model. However, I do think there is value selling consulting, services or platforms leveraging such open source tools. Not every lab, institution or even ...
written 17 months ago by Carlos Borroto • 1.5k

Latest awards to Carlos Borroto

Scholar 10 weeks ago, created an answer that has been accepted. For A: Looking for a working copy of Picard metric definitions page
Epic Question 5 months ago, created a question with more than 10,000 views. For Scientific Names In Blast Output And Databases
Epic Question 9 months ago, created a question with more than 10,000 views. For Scientific Names In Blast Output And Databases
Popular Question 9 months ago, created a question with more than 1,000 views. For In Gkno'S Fastq-Vcf Pipeline, Can I Write To Disk An Intermediary Bam Aligment Currently Sent To The Stream?
Gold Standard 14 months ago, created a post with more than 25 bookmarks. For Which Bioinformatic Friendly Pipeline Building Framework?
Teacher 15 months ago, created an answer with at least 3 up-votes. For A: Downloading multiple species from ftp.ncbi.nih.gov using wget and wildcards
Appreciated 16 months ago, created a post with more than 5 votes. For A: Scientific Names In Blast Output And Databases
Scholar 16 months ago, created an answer that has been accepted. For A: Looking for a working copy of Picard metric definitions page
Great Question 17 months ago, created a question with more than 5,000 views. For Which Bioinformatic Friendly Pipeline Building Framework?
Scholar 18 months ago, created an answer that has been accepted. For A: Looking for a working copy of Picard metric definitions page
Good Question 18 months ago, asked a question that was upvoted at least 5 times. For Scientific Names In Blast Output And Databases
Popular Question 19 months ago, created a question with more than 1,000 views. For Is There A Way To Start From 454'S ".Fna" And ".Qual" Files In Gkno?
Guru 20 months ago, received more than 100 upvotes.
Scholar 20 months ago, created an answer that has been accepted. For A: Looking for a working copy of Picard metric definitions page
Teacher 20 months ago, created an answer with at least 3 up-votes. For A: Downloading multiple species from ftp.ncbi.nih.gov using wget and wildcards
Appreciated 20 months ago, created a post with more than 5 votes. For A: Scientific Names In Blast Output And Databases
Teacher 22 months ago, created an answer with at least 3 up-votes. For A: Downloading multiple species from ftp.ncbi.nih.gov using wget and wildcards
Great Question 22 months ago, created a question with more than 5,000 views. For Scientific Names In Blast Output And Databases
Teacher 2.0 years ago, created an answer with at least 3 up-votes. For A: Downloading multiple species from ftp.ncbi.nih.gov using wget and wildcards
Appreciated 2.2 years ago, created a post with more than 5 votes. For A: Scientific Names In Blast Output And Databases
Popular Question 2.2 years ago, created a question with more than 1,000 views. For Is There A Way To Start From 454'S ".Fna" And ".Qual" Files In Gkno?
Popular Question 2.4 years ago, created a question with more than 1,000 views. For Is There A Way To Start From 454'S ".Fna" And ".Qual" Files In Gkno?
Librarian 2.5 years ago, created a post with more than 10 bookmarks. For Which Bioinformatic Friendly Pipeline Building Framework?
Prophet 2.5 years ago, created a post with more than 20 followers. For Which Bioinformatic Friendly Pipeline Building Framework?
Popular Question 2.6 years ago, created a question with more than 1,000 views. For Is There A Way To Start From 454'S ".Fna" And ".Qual" Files In Gkno?
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