User: Gabriel R.

gravatar for Gabriel R.
Gabriel R.2.7k
Reputation:
2,660
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Trusted
Location:
Danmarks Tekniske Universitet
Website:
https://grenaud.github...
Twitter:
gabrielylr
Scholar ID:
Google Scholar Page
Last seen:
17 hours ago
Joined:
7 years, 9 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.

<prev • 373 results • page 1 of 38 • next >
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Comment: C: Aligning, Sorting and Converting to bam at the same command - possible?
... not too familiar with bowtie but yes if it produces sam with a header or bam. No need to do a samtools view after, samtools sort handles bam files. Why would it be inefficient? having to wait for the entire file to sort chunks, increasing your storage 2X is more efficient? ...
written 9 days ago by Gabriel R.2.7k
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Answer: A: Insert Size For Illumina Gaiix Paired-End Library From Sam/Bam File
... I have also a super simple program in C++ built on samtools/htslib to do just that: https://github.com/grenaud/insertsize It skips sec. alignments, QC fail. you can restrict the computation to mapped or properly paired for paired reads. ...
written 6 weeks ago by Gabriel R.2.7k
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Comment: C: Fastq error compiled with ART
... which version of ART are you using? ...
written 7 weeks ago by Gabriel R.2.7k
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Answer: A: Changing Whacky Fastq Quality for Demultiplexing
... Can you try [deML][1]? It is a maximum-likelihood demultiplexer (see our paper in Bioinformatics). If you have a '@', it means a QC score of 31 which is not too far off the "normal" error rate for Illumina data? BTW, your question should not be a "forum" :-) [1]: http://grenaud.github.io/deML/ ...
written 8 weeks ago by Gabriel R.2.7k
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Comment: C: How to use trimmed and merged outputs in bwa?
... ok! let me know if you need help. network-aware-bwa can be a pain to install but I managed on a lot of systems. ...
written 8 weeks ago by Gabriel R.2.7k
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Answer: A: How to use trimmed and merged outputs in bwa?
... This is how we got around it at the Max Planck in Leipzig. This is was for ancient DNA from Neanderthals/ancient humans but should work for plants, DNA is DNA after all :-) Say we have in.fq1.gz in.fq2.gz as paired, untrimmed fastq but demultiplexed (not demultiplexed can be handle as well but nee ...
written 8 weeks ago by Gabriel R.2.7k
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Comment: C: Double Check VCF Calls in Corresponding .bam Files
... Hi Kevin, I am the author of glactools, let me know if you have any questions ...
written 8 weeks ago by Gabriel R.2.7k
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Comment: C: Convert haploid to homozygous diploid
... Great then! What you can do is to recall your variant using bcftools call and specify the option "-S, --samples-file FILE" which does: "File of sample names to include or exclude if prefixed with "^". One sample per line. See also the note above for the -s, --samples option. The sample order is upda ...
written 8 weeks ago by Gabriel R.2.7k
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Comment: C: Convert haploid to homozygous diploid
... Do you have the bams? If so, you can call bcftools with the -S, --samples-file FILE option and specify ploidy. ...
written 8 weeks ago by Gabriel R.2.7k
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Answer: A: bcf convert 23andme to vcf
... It is one line in [glactools][1], the example in the test/ folder: glactools 23andme2acf --epo epochr1.gz --fai human_g1k_v37.fasta.fai smallPublic23andMeData.gz anon | glactools glac2vcf - Probably you should replace epochr1.gz for all.epo.gz in real data. [1]: https://grenaud.github.io ...
written 3 months ago by Gabriel R.2.7k

Latest awards to Gabriel R.

Appreciated 12 weeks ago, created a post with more than 5 votes. For C: gender SNP marker
Popular Question 9 months ago, created a question with more than 1,000 views. For Merge Scaffolds From Different Individuals?
Scholar 10 months ago, created an answer that has been accepted. For A: Evolutionary distance models
Teacher 14 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 14 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 14 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 14 months ago, created a question with more than 1,000 views. For Psmc Parameters To Use
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
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
Great Question 15 months ago, created a question with more than 5,000 views. For Out Of Disk Space With Picard Tools ?
Scholar 17 months ago, created an answer that has been accepted. For A: Evolutionary distance models
Scholar 21 months ago, created an answer that has been accepted. For A: Evolutionary distance models
Popular Question 22 months ago, created a question with more than 1,000 views. For Raxml (Residues Read In Sequence)
Appreciated 22 months ago, created a post with more than 5 votes. For C: gender SNP marker
Popular Question 22 months ago, created a question with more than 1,000 views. For Create A Consensus Of Very Short Sequences
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
Scholar 2.2 years ago, created an answer that has been accepted. For A: Evolutionary distance models
Teacher 2.2 years ago, created an answer with at least 3 up-votes. For A: How To Interpret The Kmer Enrichment Plot Of A Fastqc Output
Appreciated 2.3 years ago, created a post with more than 5 votes. For C: gender SNP marker
Teacher 2.3 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 2.3 years ago, created an answer that has been accepted. For A: Evolutionary distance models
Scholar 2.4 years ago, created an answer that has been accepted. For A: Evolutionary distance models
Good Answer 2.4 years ago, created an answer that was upvoted at least 5 times. For A: What Software Programs Do Bioinformaticians Need?
Student 2.5 years ago, asked a question with at least 3 up-votes. For Out Of Disk Space With Picard Tools ?
Popular Question 2.7 years ago, created a question with more than 1,000 views. For Merge Scaffolds From Different Individuals?

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