User: Matt Miossec

gravatar for Matt Miossec
Matt Miossec350
Reputation:
350
Status:
Trusted
Location:
UK/Oxford/Wellcome Centre for human genetics
Twitter:
@RealMattJM
Last seen:
54 minutes ago
Joined:
8 years, 6 months ago
Email:
m**********@gmail.com

I am a French/American bioinformatics researcher. My doctoral thesis was in the field of Human Genetics and was conducted in the UK. Worked in Chile for close to 4 years at the centre for bioinformatics and integrative biology for 3 years. Now work at the Wellcome Centre for human genetics in Oxford.

Posts by Matt Miossec

<prev • 39 results • page 2 of 4 • next >
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Comment: C: SNP annotation of A VCF file
... Could you clarify what you mean when you say the study species have no genome? ...
written 4.8 years ago by Matt Miossec350
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Comment: C: not getting values for Filter columns with vcf files generated using SAMTOOLS Mp
... bcftools filter [OPTIONS] FILE (see:https://samtools.github.io/bcftools/bcftools.html ) ...
written 4.8 years ago by Matt Miossec350
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Answer: A: Merge BAM files without retaining sample information
... You could use the 'AddOrReplaceReadGroups' command in Picard (https://sourceforge.net/projects/picard/) to set the read group to what you want them to be in each BAM file after merging. ...
written 4.8 years ago by Matt Miossec350
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Answer: A: Genes by Protein Domain
... Any time you want to produce a list of some description, try using BioMart first:http://www.ensembl.org/biomart/ Once you've selected which gene dataset you want to look at (e.g. Homo Sapiens (GRCh38.p5) from Ensembl Genes 84), you can go to **Filters** > **PROTEIN DOMAINS AND FAMILIES** > ** ...
written 4.8 years ago by Matt Miossec350
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Comment: C: Extract Total Non-Overlapping Exon Length Per Gene With Bioconductor
... I've tried this and it might not be the best idea. When creating a GTF-file, the UCSC table browser fills in the gene_ID field with the transcript_ID, no matter whether the UCSC, RefSeq or Ensembl track is used, which defeats the purpose of your script. I have no idea why UCSC would do this, seems l ...
written 4.8 years ago by Matt Miossec350
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Answer: A: retrieval of population specific SNPs
... You'll want to use the Exome Aggregation Consortium (ExAC) Data Set: http://exac.broadinstitute.org/ to get the sub-population frequencies for all your SNPs. The frequencies are based on a very large data set (60,706 unrelated individuals). If you have the position, reference and variant allele for ...
written 4.8 years ago by Matt Miossec350
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Comment: C: Question about ExomeDepth's output
... Could it be protein start and end perhaps? ...
written 6.7 years ago by Matt Miossec350
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Comment: C: how to select candidate genes after resequencing
... This paper might give you some helpful pointers: Detecting Selective Sweeps from Pooled Next-Generation Sequencing Samples ...
written 6.7 years ago by Matt Miossec350
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Answer: A: Looking for individual genome browsers
... Would this be what you're looking for? http://huref.jcvi.org/ (Craig Venter) ...
written 6.7 years ago by Matt Miossec350
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Comment: C: How Large Can A Coverage Discrepancy Be Between Two Aligners, Specifically Bwa A
... Thanks, I'll check. ...
written 7.5 years ago by Matt Miossec350

Latest awards to Matt Miossec

Popular Question 4.2 years ago, created a question with more than 1,000 views. For Does Samtools Tview Hide Pcr And Optical Duplicates?
Voter 4.8 years ago, voted more than 100 times.
Scholar 4.8 years ago, created an answer that has been accepted. For A: Genes by Protein Domain
Teacher 4.8 years ago, created an answer with at least 3 up-votes. For A: Genes by Protein Domain
Scholar 4.8 years ago, created an answer that has been accepted. For A: Genes by Protein Domain
Teacher 4.8 years ago, created an answer with at least 3 up-votes. For A: Rare Variant Snps With No Allele Frequency
Popular Question 5.0 years ago, created a question with more than 1,000 views. For Does Samtools Tview Hide Pcr And Optical Duplicates?
Popular Question 6.0 years ago, created a question with more than 1,000 views. For Does Anybody Know Which Gatk Walkers Are Positively Affected By Pedigree Information?
Supporter 6.9 years ago, voted at least 25 times.
Teacher 6.9 years ago, created an answer with at least 3 up-votes. For A: Rare Variant Snps With No Allele Frequency
Autobiographer 6.9 years ago, has more than 80 characters in the information field of the user's profile.

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