User: Pablo Marin-Garcia

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1,680
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Location:
Spain
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Last seen:
1 month, 2 weeks ago
Joined:
5 years, 11 months ago
Email:
h*************@gmail.com

Currently I work as an analyst and bioinformatician in human genetics at FHCUV-INCLIVA in Valencia (Spain). I have been working 9 years at Sanger Center and European Bioinformatics Institute (Cambridge, UK) dealing with genomic analysis of complex diseases in humans.

I have a Zoology degree, a master in genetics and evolution and a PhD in molecular genetics in complex diseases (Hypertension) and a master in biomedicine statistics.

I create software applications for genetic analysis and genomic visualization using Perl (bioperl API, ensEMBL API), R (bioconductor) and javascript (jquery and extjs)

Posts by Pablo Marin-Garcia

<prev • 92 results • page 1 of 10 • next >
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Comment: C: Cheat Sheet For One-Based Vs Zero-Based Coordinate Systems
... In ENSEMBL they treat the INS giving start>end: http://www.ensembl.org/info/docs/tools/vep/vep_formats.html#vcf The following examples illustrate how VCF describes a variant and how it is handled internally by VEP. Consider the following aligned sequences (for the purposes of discussion on chrom ...
written 3 months ago by Pablo Marin-Garcia1.7k
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Answer: A: Sequence Clustering Based On Similarity
... this question was cross-posted and answered at http://seqanswers.com/forums/showthread.php?t=31750 > Perhaps USEARCH[1] or if you want something much more complicated, OrthoMCL.[1]. [1] http://www.drive5.com/usearch/ [2] http://orthomcl.org/common/downloads/software/v2.0/ ...
written 5 months ago by Pablo Marin-Garcia1.7k
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Answer: A: Add Dp Tag To Genotype Field Of Vcf File
... Just to keep this updated for samtools 1.2 onwards the -D is deprecated now there is an option --output-tag DP For samptools 1.2,  mpilup -t has DP,DPR,DV,DP4,INFO/DPR,SP for 1.3 DP4 has changed to ADF (Allelic depths on the forward strand, FORMAT) and ADR (Allelic depths on the reverse strand, FO ...
written 13 months ago by Pablo Marin-Garcia1.7k
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Comment: C: get biotype for refseq NM transcripts
... Thanks Emily i took me some time to find it out after posting the question. Never come across a XR thanks for that one. I wish this nomenclature were more easy to find when you google for refseq transcript nomenclature. You go to  http://www.ncbi.nlm.nih.gov/refseq/about/ and you can read only abo ...
written 20 months ago by Pablo Marin-Garcia1.7k
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Comment: C: get biotype for refseq NM transcripts
... For some aplications I use refseq and HGMD, both using NM. Has Ensembl already solved the problems mapping/integrating refseqs ids? ...
written 20 months ago by Pablo Marin-Garcia1.7k
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Comment: C: get biotype for refseq NM transcripts
... Does the NM have biotype labels as diverse as ensembl has? ...
written 20 months ago by Pablo Marin-Garcia1.7k
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Comment: C: get biotype for refseq NM transcripts
... NM=mRNA  NR=RNA from NCBI tutorials. When you think it twice, it make sense to read it as NR not-mRNA http://www.ncbi.nlm.nih.gov/books/NBK21091/table/ch18.T.refseq_accession_numbers_and_mole/?report=objectonly ...
written 20 months ago by Pablo Marin-Garcia1.7k
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Comment: C: get biotype for refseq NM transcripts
... I saw that in wikipedia NR is for non coding, but I read somewareelse that NR was for predicted transcripts, so I was not sure. ...
written 20 months ago by Pablo Marin-Garcia1.7k
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Comment: C: get biotype for refseq NM transcripts
... "protein coding genes" was a misstype I wanted to say 'transcript'. I wanted to double check how to filter the NM_ list from a gene, for the ones that are for real and 'functional' transcripts. Also I would like to query in which tissue are they the primary transcript if any. Probably expression atl ...
written 20 months ago by Pablo Marin-Garcia1.7k
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get biotype for refseq NM transcripts
... I woudl like to have the biotypes (like in ensembl transcripts) but for the NCBI refSeq downloaded from UCSC mysql. Which table should I join and which column should I use? My current query without the biotype is:        mysql --user=genome --host=genome-mysql.cse.ucsc.edu -u genome -D hg19 -N -A ...
refseq written 20 months ago by Pablo Marin-Garcia1.7k • updated 20 months ago by Dan Gaston6.6k

Latest awards to Pablo Marin-Garcia

Popular Question 3 months ago, created a question with more than 1,000 views. For Is The Bwa Reference Indexing The Same Thing That Fasta Indexing With Samtools?
Popular Question 4 months ago, created a question with more than 1,000 views. For Is The Bwa Reference Indexing The Same Thing That Fasta Indexing With Samtools?
Popular Question 6 months ago, created a question with more than 1,000 views. For Why Import Command In Samtools Is Not Shown In The Short Help Of Samtools?
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Popular Question 12 months ago, created a question with more than 1,000 views. For 1000 Genomes Human Reference Assembly File With Non Actgn Chars In Chr 3, Why?
Student 12 months ago, asked a question with at least 3 up-votes. For Is The Bwa Reference Indexing The Same Thing That Fasta Indexing With Samtools?
Popular Question 12 months ago, created a question with more than 1,000 views. For Is The Bwa Reference Indexing The Same Thing That Fasta Indexing With Samtools?
Student 12 months ago, asked a question with at least 3 up-votes. For 1000 Genomes Human Reference Assembly File With Non Actgn Chars In Chr 3, Why?
Popular Question 18 months ago, created a question with more than 1,000 views. For Given A Fastq File, Is It Possible To Know If It Comes From Paired Or Single End?
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Popular Question 22 months ago, created a question with more than 1,000 views. For Is The Bwa Reference Indexing The Same Thing That Fasta Indexing With Samtools?
Student 22 months ago, asked a question with at least 3 up-votes. For Why Import Command In Samtools Is Not Shown In The Short Help Of Samtools?
Popular Question 2.2 years ago, created a question with more than 1,000 views. For Is The Bwa Reference Indexing The Same Thing That Fasta Indexing With Samtools?
Good Answer 2.2 years ago, created an answer that was upvoted at least 5 times. For A: Distributing And Tracking Work Among Bioinformaticians
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Popular Question 2.2 years ago, created a question with more than 1,000 views. For Which Program Do You Use For Converting Srf (Short Read Format) To Fastq?
Good Answer 2.4 years ago, created an answer that was upvoted at least 5 times. For A: Distributing And Tracking Work Among Bioinformaticians
Good Answer 2.5 years ago, created an answer that was upvoted at least 5 times. For A: Distributing And Tracking Work Among Bioinformaticians
Appreciated 2.5 years ago, created a post with more than 5 votes. For C: Should General Programming Questions Actually Be Posted To Biostar?
Teacher 2.5 years ago, created an answer with at least 3 up-votes. For A: Why Import Command In Samtools Is Not Shown In The Short Help Of Samtools?
Appreciated 2.5 years ago, created a post with more than 5 votes. For C: Should General Programming Questions Actually Be Posted To Biostar?
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Good Question 2.8 years ago, asked a question that was upvoted at least 5 times. For Is Zlib Library Failing To Process Properly Bgzip Files?

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