User: Carlos Borroto

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Carlos Borroto1.5k
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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 • 81 results • page 1 of 9 • next >
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Answer: A: Problem Downloading The Nt Database From Ncbi
... In case someone finds this thread while searching for this issue, you can ask update_blastdb to use passive mode. $ update_blastdb --passive --decompress nt ...
written 23 days ago by Carlos Borroto1.5k
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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 6 months ago by Carlos Borroto1.5k
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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 9 months ago by Carlos Borroto1.5k
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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 17 months ago by Carlos Borroto1.5k
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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 18 months ago by Carlos Borroto1.5k
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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 18 months ago by Carlos Borroto1.5k
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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 18 months ago by Carlos Borroto1.5k
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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 19 months ago by Carlos Borroto1.5k
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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 19 months ago by Carlos Borroto1.5k
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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 19 months ago by Carlos Borroto1.5k

Latest awards to Carlos Borroto

Appreciated 22 days ago, created a post with more than 5 votes. For A: FreeBayes vs GATK's HaplotypeCaller
Scholar 4 months ago, created an answer that has been accepted. For A: Looking for a working copy of Picard metric definitions page
Epic Question 7 months ago, created a question with more than 10,000 views. For Scientific Names In Blast Output And Databases
Epic Question 11 months ago, created a question with more than 10,000 views. For Scientific Names In Blast Output And Databases
Gold Standard 16 months ago, created a post with more than 25 bookmarks. For Which Bioinformatic Friendly Pipeline Building Framework?
Teacher 18 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 18 months ago, created a post with more than 5 votes. For A: Scientific Names In Blast Output And Databases
Scholar 18 months ago, created an answer that has been accepted. For A: Looking for a working copy of Picard metric definitions page
Great Question 19 months ago, created a question with more than 5,000 views. For Which Bioinformatic Friendly Pipeline Building Framework?
Scholar 20 months ago, created an answer that has been accepted. For A: Looking for a working copy of Picard metric definitions page
Good Question 20 months ago, asked a question that was upvoted at least 5 times. For Scientific Names In Blast Output And Databases
Popular Question 22 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 22 months ago, received more than 100 upvotes.
Scholar 22 months ago, created an answer that has been accepted. For A: Looking for a working copy of Picard metric definitions page
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
Appreciated 22 months ago, created a post with more than 5 votes. For A: Scientific Names In Blast Output And Databases
Teacher 24 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 2.0 years ago, created a question with more than 5,000 views. For Scientific Names In Blast Output And Databases
Teacher 2.2 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 2.4 years ago, created a post with more than 5 votes. For A: Scientific Names In Blast Output And Databases
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?
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?
Librarian 2.6 years ago, created a post with more than 10 bookmarks. For Which Bioinformatic Friendly Pipeline Building Framework?
Prophet 2.6 years ago, created a post with more than 20 followers. For Which Bioinformatic Friendly Pipeline Building Framework?

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