User: Gabriel R.
Gabriel R. • 2.8k
- Reputation:
- 2,750
- Status:
- Trusted
- Location:
- Danmarks Tekniske Universitet
- Website:
- https://grenaud.github...
- Twitter:
- gabrielylr
- Scholar ID:
- Google Scholar Page
- Last seen:
- 5 hours ago
- Joined:
- 8 years, 6 months ago
- Email:
- m***************@yahoo.com
I am assistant professor at the Technical University of Denmark. In a former life, I was postdoc at the Center for Geogenetics at Copenhagen University and before, 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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... not in R but in C++:
https://github.com/shahcompbio/hmmcopy_utils
I guess you could automate calls in R? ...
written 10 days ago by
Gabriel R. • 2.8k
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5.2k
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Comment:
C: Demultiplexing Illumina data
... could you post the offending line? Put 4 whitespaces before the line to keep the format. ...
written 22 days ago by
Gabriel R. • 2.8k
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... I have coded a subroutine to rebuild the ref. from the CIGAR+MD using htslib, never again! I reuse that code over and over. I would have loved your tool when I was developing my code, it would have saved me a lot of time. I am sure a programmer will enjoy it in the future ;-) ...
written 24 days ago by
Gabriel R. • 2.8k
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... very useful little tool btw! ...
written 24 days ago by
Gabriel R. • 2.8k
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153
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... ah great! I only read your biostars post :-)
...
written 27 days ago by
Gabriel R. • 2.8k
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... nice! maybe point out that you need the MD field to be correct. doesn't it? ...
written 27 days ago by
Gabriel R. • 2.8k
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Comment:
C: filter illumina index
... Just so I can understand, could you post examples of sequences you have and a list of expected indices? ...
written 6 weeks ago by
Gabriel R. • 2.8k
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... I copied your file as "biostars.fq.gz"
First extract your first indices:
zcat biostars.fq.gz |awk '{if( (NR%4)==1){ print $0; print substr($2,length($2)-16,8); print "+"; print "FFFFFFFF"} }' |gzip > index1.fq.gz
Second extract the second:
zcat biostars.fq.gz |awk '{if( (NR%4)==1){ ...
written 4 months ago by
Gabriel R. • 2.8k
• updated
4 months ago by
genomax ♦ 91k
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315
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... Normally, you should put them as a separate file. However, you can transform your indices in the header into separate files easily using UNIX commands. If you need a hand, paste a few sequences with the headers and I can have a look. ...
written 4 months ago by
Gabriel R. • 2.8k
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315
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... let me know if you need help!
...
written 4 months ago by
Gabriel R. • 2.8k
Latest awards to Gabriel R.
Good Answer
4 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
5 months ago,
created a question with more than 1,000 views.
For DICE: Joint Estimation of Contamination, Error and Demography for Nuclear DNA from Ancient Humans
Popular Question
18 months ago,
created a question with more than 1,000 views.
For Merge Scaffolds From Different Individuals?
Scholar
19 months ago,
created an answer that has been accepted.
For A: Evolutionary distance models
Teacher
23 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
23 months 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
23 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
23 months ago,
created a question with more than 1,000 views.
For Psmc Parameters To Use
Teacher
2.0 years ago,
created an answer with at least 3 up-votes.
For A: How To Interpret The Kmer Enrichment Plot Of A Fastqc Output
Teacher
2.0 years 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
2.1 years ago,
created a question with more than 5,000 views.
For Out Of Disk Space With Picard Tools ?
Scholar
2.2 years ago,
created an answer that has been accepted.
For A: Evolutionary distance models
Scholar
2.5 years ago,
created an answer that has been accepted.
For A: Evolutionary distance models
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2.6 years ago,
created a question with more than 1,000 views.
For Raxml (Residues Read In Sequence)
Popular Question
2.6 years ago,
created a question with more than 1,000 views.
For Create A Consensus Of Very Short Sequences
Teacher
2.7 years ago,
created an answer with at least 3 up-votes.
For A: How To Interpret The Kmer Enrichment Plot Of A Fastqc Output
Scholar
3.0 years ago,
created an answer that has been accepted.
For A: Evolutionary distance models
Teacher
3.0 years ago,
created an answer with at least 3 up-votes.
For A: How To Interpret The Kmer Enrichment Plot Of A Fastqc Output
Scholar
3.1 years ago,
created an answer that has been accepted.
For A: Evolutionary distance models
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