User: Gabriel R.

gravatar for Gabriel R.
Gabriel R.2.5k
Reputation:
2,450
Status:
Trusted
Location:
Center for Geogenetik Københavns Universitet
Website:
https://grenaud.github...
Twitter:
gabrielylr
Scholar ID:
Google Scholar Page
Last seen:
20 hours ago
Joined:
6 years, 4 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.

<prev • 331 results • page 1 of 34 • next >
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Comment: C: Calculate average mapping quality at a position
... it depends on the aligner but it in any case, it's a bit of a scam: https://sequencing.qcfail.com/articles/mapq-values-are-really-useful-but-their-implementation-is-a-mess/ The link above has a plot of the distribution of mapping qualities. ...
written 8 days ago by Gabriel R.2.5k
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Comment: C: Calculate average mapping quality at a position
... I think this is using "samtools mpileup -s" which outputs the base quality followed by the mapping qualities for the read that supports the base. ...
written 9 days ago by Gabriel R.2.5k
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Answer: A: Calculate average mapping quality at a position
... These are probabilities of mismapping on a PHRED scale. For the first one, the probability of mismapping is: (10^(-(39/10)) = 0.0001258925 For the second it is: 10^(-(50/10)) = 1e-05 So on average, your probability of mismapping is: (0.0001258925+1e-05)/2 = 6.794627e-05 On a PHRE ...
written 9 days ago by Gabriel R.2.5k
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Comment: C: TCGA SNP to plink
... Could you send a direct link to the MAF file you want to convert? ...
written 4 weeks ago by Gabriel R.2.5k
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Comment: C: Convert beagle output file to plink
... I just saw, this can you please provide a link to the format that you have? ...
written 8 weeks ago by Gabriel R.2.5k
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Comment: C: samtools and I/O redirection
... let's take a step back, why do you want a sam file to begin with? ...
written 9 weeks ago by Gabriel R.2.5k
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Comment: C: Plink to Treemix
... I am not sure about your problem but you could import your plink file into [glactools][1], do the filtering and export to treemix. [1]: https://grenaud.github.io/glactools/ ...
written 10 weeks ago by Gabriel R.2.5k
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Comment: C: How to convert BAF to SNP genotype A/B
... could you post an example of the input? ...
written 11 weeks ago by Gabriel R.2.5k
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Comment: C: How to add RG tag into the optional field in a BAM file
... 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 12 weeks ago by Gabriel R.2.5k
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Comment: C: How to add RG tag into the optional field in a BAM file
... 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 12 weeks ago by Gabriel R.2.5k

Latest awards to Gabriel R.

Scholar 9 days ago, created an answer that has been accepted. For A: Evolutionary distance models
Scholar 3 months ago, created an answer that has been accepted. For A: Evolutionary distance models
Popular Question 5 months ago, created a question with more than 1,000 views. For Raxml (Residues Read In Sequence)
Appreciated 5 months ago, created a post with more than 5 votes. For C: gender SNP marker
Popular Question 5 months ago, created a question with more than 1,000 views. For Create A Consensus Of Very Short Sequences
Teacher 5 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 9 months ago, created an answer that has been accepted. For A: Evolutionary distance models
Teacher 9 months ago, created an answer with at least 3 up-votes. For A: How To Interpret The Kmer Enrichment Plot Of A Fastqc Output
Appreciated 10 months ago, created a post with more than 5 votes. For C: gender SNP marker
Scholar 10 months ago, created an answer that has been accepted. For A: Evolutionary distance models
Teacher 10 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 12 months ago, created an answer that has been accepted. For A: Evolutionary distance models
Good Answer 12 months ago, created an answer that was upvoted at least 5 times. For A: What Software Programs Do Bioinformaticians Need?
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Popular Question 21 months ago, created a question with more than 1,000 views. For Duplicate Removal Of New Sequence Data?
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Scholar 2.0 years ago, created an answer that has been accepted. For A: Evolutionary distance models
Appreciated 2.0 years ago, created a post with more than 5 votes. For C: gender SNP marker
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