User: Pablo Marin-Garcia

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Spain
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Last seen:
2 months, 1 week ago
Joined:
8 years, 7 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 • 94 results • page 1 of 10 • next >
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Answer: A: Fisher Strand in GATK, a good measure to detect Strand Bias?
... One nice explanation could be found in [this samtools mailing list post][1] If you have only reads in one strand you can not "have" strand bias, or at least you can not measure it, since the other strand has 0 reads. The strand bias measure if the proportion of alleles is statistically different b ...
written 9 weeks ago by Pablo Marin-Garcia1.8k
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Answer: A: Calculation of VAF (variant allele frequency)
... **MAF** = minor allele frequency, is the frequency of these allele in the POPULATION. you have a bunch of samples genotyped and then: 1- you calculate the frequency of one of the alleles (usually the non-reference allele) for a given variant: ``` freq(a) =( sum(samples_with_geno_aa x 2) + su ...
written 9 months ago by Pablo Marin-Garcia1.8k
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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 2.9 years ago by Pablo Marin-Garcia1.8k
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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 3.1 years ago by Pablo Marin-Garcia1.8k
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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 3.8 years ago by Pablo Marin-Garcia1.8k
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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 4.3 years ago by Pablo Marin-Garcia1.8k
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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 4.3 years ago by Pablo Marin-Garcia1.8k
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Comment: C: get biotype for refseq NM transcripts
... Does the NM have biotype labels as diverse as ensembl has? ...
written 4.3 years ago by Pablo Marin-Garcia1.8k
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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 4.3 years ago by Pablo Marin-Garcia1.8k
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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 4.3 years ago by Pablo Marin-Garcia1.8k

Latest awards to Pablo Marin-Garcia

Teacher 9 months ago, created an answer with at least 3 up-votes. For A: Piping With Samtools, Bwa And Bedtools
Student 2.3 years ago, asked a question with at least 3 up-votes. For get biotype for refseq NM transcripts
Popular Question 2.3 years ago, created a question with more than 1,000 views. For get biotype for refseq NM transcripts
Popular Question 2.9 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?
Popular Question 3.0 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?
Popular Question 3.2 years 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?
Great Question 3.2 years ago, created a question with more than 5,000 views. For Casava 1.8 Vs Gatk
Popular Question 3.6 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?
Student 3.6 years ago, asked a question with at least 3 up-votes. For Is The Bwa Reference Indexing The Same Thing That Fasta Indexing With Samtools?
Student 3.6 years 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 3.6 years 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?
Popular Question 4.2 years 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?
Popular Question 4.2 years 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?
Popular Question 4.3 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?
Student 4.5 years 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 4.5 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?
Popular Question 4.8 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?
Student 4.8 years ago, asked a question with at least 3 up-votes. For Could You Trust The Bam Header So:Coordinate?
Good Answer 4.8 years ago, created an answer that was upvoted at least 5 times. For A: Distributing And Tracking Work Among Bioinformaticians
Popular Question 4.8 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?
Teacher 4.8 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?
Good Answer 5.0 years ago, created an answer that was upvoted at least 5 times. For A: Distributing And Tracking Work Among Bioinformaticians
Good Answer 5.1 years ago, created an answer that was upvoted at least 5 times. For A: Distributing And Tracking Work Among Bioinformaticians
Appreciated 5.1 years ago, created a post with more than 5 votes. For C: Should General Programming Questions Actually Be Posted To Biostar?
Teacher 5.1 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?

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