User: Gabriel R.
Gabriel R. • 2.4k
- Reputation:
- 2,390
- Status:
- Trusted
- Location:
- Center for Geogenetik Københavns Universitet
- Website:
- https://grenaud.github...
- Twitter:
- gabrielylr
- Scholar ID:
- Google Scholar Page
- Last seen:
- 2 hours ago
- Joined:
- 6 years, 1 month 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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... ok lets try the following:
1) sort your bam files wrt read names, NOT coordinates.
2) run the following:
samtools view sortedWRTnames.bam | awk '{ if(substr($1,1,1)=="@"){print $0}else{ idx=substr($1,0,12); printf("%s\t", substr($1,14)); for(i=2;i<=NF;i++){ printf("%s\t",$i); } printf("XI ...
written 1 day ago by
Gabriel R. • 2.4k
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... yes I am aware. This is essentially a demultiplexing problem. if no one answers by the end of the day, I could be cajoled into making a slight modification to deML to account for this. ...
written 1 day ago by
Gabriel R. • 2.4k
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... Do you have a correspondence between the barcode and read group? ex:
CAACCATCACTC sample10 ...
written 1 day ago by
Gabriel R. • 2.4k
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114
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... did you try it? did it work? ...
written 7 days ago by
Gabriel R. • 2.4k
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... I can code a module to import them using glactools and export in plink. We currently do not support this format but I could code it. ...
written 7 days ago by
Gabriel R. • 2.4k
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... but they could potentially be: 0.5 0.5 0? just to be sure. ...
written 7 days ago by
Gabriel R. • 2.4k
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... and I imagine these probabilities are not just 0 and 1 but can be 0.4 for example? But they have to sum up to 1 I suppose. ...
written 8 days ago by
Gabriel R. • 2.4k
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114
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... and you have a sample file as well? are these files simply zipped and not binary? ...
written 8 days ago by
Gabriel R. • 2.4k
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114
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... could you post a small subset of your file somewhere? ...
written 8 days ago by
Gabriel R. • 2.4k
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114
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... is this the output file format: http://www.stats.ox.ac.uk/~marchini/software/gwas/file_format.html ? ...
written 8 days ago by
Gabriel R. • 2.4k
Latest awards to Gabriel R.
Popular Question
9 weeks ago,
created a question with more than 1,000 views.
For Raxml (Residues Read In Sequence)
Popular Question
9 weeks ago,
created a question with more than 1,000 views.
For Create A Consensus Of Very Short Sequences
Teacher
12 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
6 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
7 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
9 months ago,
created an answer that was upvoted at least 5 times.
For A: What Software Programs Do Bioinformaticians Need?
Student
9 months ago,
asked a question with at least 3 up-votes.
For Out Of Disk Space With Picard Tools ?
Popular Question
12 months ago,
created a question with more than 1,000 views.
For Merge Scaffolds From Different Individuals?
Epic Question
12 months ago,
created a question with more than 10,000 views.
For Out Of Disk Space With Picard Tools ?
Good Question
15 months ago,
asked a question that was upvoted at least 5 times.
For Out Of Disk Space With Picard Tools ?
Popular Question
18 months ago,
created a question with more than 1,000 views.
For Duplicate Removal Of New Sequence Data?
Popular Question
20 months ago,
created a question with more than 1,000 views.
For Chry In 1000G Vs Hg19
Scholar
21 months ago,
created an answer that has been accepted.
For A: Evolutionary distance models
Teacher
21 months ago,
created an answer with at least 3 up-votes.
For A: How To Write A Perl Script To Transform A Sequence In A Tabular File Into A Fast
Voter
22 months ago,
voted more than 100 times.
Scholar
23 months ago,
created an answer that has been accepted.
For A: Evolutionary distance models
Appreciated
23 months ago,
created a post with more than 5 votes.
For A: Should I Do A Dual Master Degree In Both Bioinformatics And Cs?
Teacher
23 months ago,
created an answer with at least 3 up-votes.
For A: How To Write A Perl Script To Transform A Sequence In A Tabular File Into A Fast
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