User: Gabriel R.
Gabriel R. • 2.5k
- Reputation:
- 2,530
- Status:
- Trusted
- Location:
- Center for Geogenetik Københavns Universitet
- Website:
- https://grenaud.github...
- Twitter:
- gabrielylr
- Scholar ID:
- 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.
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... 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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... 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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... how bad would it be to restrict the analysis to transversions? ...
written 11 days ago by
Gabriel R. • 2.5k
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... 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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... 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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... 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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... 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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... can you post a few sequences somewhere? ...
written 8 weeks ago by
Gabriel R. • 2.5k
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... 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 ?
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
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15 months ago,
created an answer that has been accepted.
For A: Evolutionary distance models
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,
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For Out Of Disk Space With Picard Tools ?
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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,
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For Duplicate Removal Of New Sequence Data?
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