User: Gabriel R.

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Gabriel R.2.5k
Reputation:
2,530
Status:
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Location:
Center for Geogenetik Københavns Universitet
Website:
https://grenaud.github...
Twitter:
gabrielylr
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Google Scholar Page
Last seen:
1 day, 21 hours ago
Joined:
6 years, 10 months ago
Email:
m***************@yahoo.com

Now postdoc at the Center for Geogenetics at Copenhagen University. In a former life, I was a Ph.D student in bioinformatics at the Max Planck Institute for Evolutionary Anthropology/ Interested in sequencing, particularly ancient DNA and inference of demography. 

Posts by Gabriel R.

<prev • 343 results • page 1 of 35 • next >
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Comment: C: Vcftools r2 Error: Insufficient sites remained after filtering or No data left
... In my case, I saw that I had a non-phased individual that had been merged with the phased ones and all sites got removed as a result. ...
written 8 days ago by Gabriel R.2.5k
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Comment: C: Variant calling using IonTorrent caller correcting for deamination
... can I ask you, could you plot the damage? Also, could you post a bit of the data somewhere and msg me, I have never had my hands on IonTorrent aDNA before. ...
written 11 days ago by Gabriel R.2.5k
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Comment: C: Variant calling using IonTorrent caller correcting for deamination
... how bad would it be to restrict the analysis to transversions? ...
written 11 days ago by Gabriel R.2.5k
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Comment: C: Converting Eigenstrat format to G-phocs-input format
... just a comment, often eigenstrat format only contains variant sites whereas G-PhoCS uses all sites in a locus. ...
written 4 weeks ago by Gabriel R.2.5k
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Answer: A: Low coverage genome simulation
... We created a set of programs called gargammel that can simulate the reads once you have the fasta file of the genome: [gargammel on github][1] [here is the paper][2] For simulating demographies, I have been using msprime. [1]: http://grenaud.github.io/gargammel/ [2]: https://academic.oup.com ...
written 8 weeks ago by Gabriel R.2.5k
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Comment: C: What do you consider to be raw data from Illumina sequencers? Possible legacy d
... a comment, @genomemax is correct with his graph, it presents some of the old file formats. Illumina has changed the way it represents its internal data a few times. Good luck! ...
written 8 weeks ago by Gabriel R.2.5k
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Answer: A: What do you consider to be raw data from Illumina sequencers? Possible legacy d
... There are different layers of raw data way before demultiplexing: 1. The files at the most basic layer are raw images, those are massive. 2. After image analysis, you have intensity for each cluster, those are normally in .cif format. They do not contain bases but raw intensity. 3. After baseca ...
written 8 weeks ago by Gabriel R.2.5k
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Comment: C: Trimmomatic not trimming the adapter
... can you post a few sequences somewhere? ...
written 8 weeks ago by Gabriel R.2.5k
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Answer: A: Demultiplexing before merging paired-end reads?
... This post is between a comment and a response. I work a lot with ancient DNA where fragments are very short (e.g. 40bp). This entails that even for a paired-end run you constantly have to deal with "single-end" reads (merged paired-end) and genuine paired-end data. The logic was getting very convolu ...
written 3 months ago by Gabriel R.2.5k
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Comment: C: reference genome hs37d5 with PhiX
... I am no longer there, I will ask my former supervisor, let's see if they can stick it somewhere. in the meantime, here are the accessions for the reference: http://cdna.eva.mpg.de/neandertal/Chagyrskaya/bam/README ...
written 4 months ago by Gabriel R.2.5k

Latest awards to Gabriel R.

Teacher 11 weeks ago, created an answer with at least 3 up-votes. For A: How To Interpret The Kmer Enrichment Plot Of A Fastqc Output
Teacher 11 weeks ago, created an answer with at least 3 up-votes. For A: How To Interpret The Kmer Enrichment Plot Of A Fastqc Output
Good Answer 3 months ago, created an answer that was upvoted at least 5 times. For A: What Skills Do You Have To Have As A Phd Graduate In Bioinformatics?
Popular Question 3 months ago, created a question with more than 1,000 views. For Psmc Parameters To Use
Teacher 4 months ago, created an answer with at least 3 up-votes. For A: How To Interpret The Kmer Enrichment Plot Of A Fastqc Output
Teacher 4 months ago, created an answer with at least 3 up-votes. For A: How To Interpret The Kmer Enrichment Plot Of A Fastqc Output
Great Question 4 months ago, created a question with more than 5,000 views. For Out Of Disk Space With Picard Tools ?
Scholar 6 months ago, created an answer that has been accepted. For A: Evolutionary distance models
Scholar 9 months ago, created an answer that has been accepted. For A: Evolutionary distance models
Appreciated 11 months ago, created a post with more than 5 votes. For C: gender SNP marker
Popular Question 11 months ago, created a question with more than 1,000 views. For Raxml (Residues Read In Sequence)
Popular Question 11 months ago, created a question with more than 1,000 views. For Create A Consensus Of Very Short Sequences
Teacher 11 months ago, created an answer with at least 3 up-votes. For A: How To Interpret The Kmer Enrichment Plot Of A Fastqc Output
Teacher 15 months ago, created an answer with at least 3 up-votes. For A: How To Interpret The Kmer Enrichment Plot Of A Fastqc Output
Scholar 15 months ago, created an answer that has been accepted. For A: Evolutionary distance models
Appreciated 16 months ago, created a post with more than 5 votes. For C: gender SNP marker
Scholar 16 months ago, created an answer that has been accepted. For A: Evolutionary distance models
Teacher 16 months ago, created an answer with at least 3 up-votes. For A: How To Interpret The Kmer Enrichment Plot Of A Fastqc Output
Scholar 18 months ago, created an answer that has been accepted. For A: Evolutionary distance models
Good Answer 18 months ago, created an answer that was upvoted at least 5 times. For A: What Software Programs Do Bioinformaticians Need?
Student 18 months ago, asked a question with at least 3 up-votes. For Out Of Disk Space With Picard Tools ?
Popular Question 21 months ago, created a question with more than 1,000 views. For Merge Scaffolds From Different Individuals?
Epic Question 21 months ago, created a question with more than 10,000 views. For Out Of Disk Space With Picard Tools ?
Good Question 2.0 years ago, asked a question that was upvoted at least 5 times. For Out Of Disk Space With Picard Tools ?
Popular Question 2.3 years ago, created a question with more than 1,000 views. For Duplicate Removal Of New Sequence Data?

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