User: Gabriel R.
Gabriel R. • 2.7k
- Reputation:
- 2,690
- Status:
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- Location:
- Danmarks Tekniske Universitet
- Website:
- https://grenaud.github...
- Twitter:
- gabrielylr
- Scholar ID:
- Google Scholar Page
- Last seen:
- 5 hours ago
- Joined:
- 8 years, 1 month 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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... samtools view -b input.sorted.bam `samtools view -H input.sorted.bam |grep "^@SQ" |cut -f 2,3 |sed "s/.N://g" |awk '{if($2>1000){print $1}}' |tr "\n" " "` > input.longcontig.sorted.bam
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written 3 days ago by
Gabriel R. • 2.7k
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... There is no single answer, in a relatively "old" paper, back from 2000:
[Mitochondrial genome variation and
the origin of modern humans][1]
I would look at Table 1, you have the ; MPSD, mean pairwise sequence difference, the result varies a lot depending on whether you look at Africans vs non-Afri ...
written 3 days ago by
Gabriel R. • 2.7k
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Comment:
C: Calling chrMT only from BAM
... I have editted my post with "mitochondrial modern" and "mitochondrial ancient" to make it clear that I mean mitochondrial. Apologies for the confusion! ...
written 7 weeks ago by
Gabriel R. • 2.7k
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Answer:
A: Calling chrMT only from BAM
... We published a caller for mitochondrial ancient DNA but it is suitable for mitochondrial modern DNA as well. For mitochondrial modern DNA the problem is even simpler. The name of the program is **endoCaller** part of the ([schmutzi package][1])
You can call it as such:
endoCaller -seq cons ...
written 7 weeks ago by
Gabriel R. • 2.7k
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... 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 4 months ago by
Gabriel R. • 2.7k
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... 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 5 months 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 6 months ago by
Gabriel R. • 2.7k
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... 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 6 months ago by
Gabriel R. • 2.7k
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... 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 6 months ago by
Gabriel R. • 2.7k
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189
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... 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 6 months ago by
Gabriel R. • 2.7k
Latest awards to Gabriel R.
Popular Question
25 days 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
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13 months ago,
created a question with more than 1,000 views.
For Merge Scaffolds From Different Individuals?
Scholar
14 months ago,
created an answer that has been accepted.
For A: Evolutionary distance models
Teacher
18 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
18 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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18 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
18 months ago,
created a question with more than 1,000 views.
For Psmc Parameters To Use
Teacher
19 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
19 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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20 months ago,
created a question with more than 5,000 views.
For Out Of Disk Space With Picard Tools ?
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21 months ago,
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For A: Evolutionary distance models
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2.1 years ago,
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For A: Evolutionary distance models
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2.2 years ago,
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For Raxml (Residues Read In Sequence)
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2.2 years ago,
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For Create A Consensus Of Very Short Sequences
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2.2 years ago,
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For A: How To Interpret The Kmer Enrichment Plot Of A Fastqc Output
Teacher
2.6 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
2.6 years ago,
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For A: Evolutionary distance models
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2.6 years ago,
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For A: How To Interpret The Kmer Enrichment Plot Of A Fastqc Output
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2.6 years ago,
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For A: Evolutionary distance models
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2.8 years ago,
created an answer that has been accepted.
For A: Evolutionary distance models
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