User: Gabriel R.

gravatar for Gabriel R.
Gabriel R.2.6k
Reputation:
2,590
Status:
Trusted
Location:
Center for Geogenetik Københavns Universitet
Website:
https://grenaud.github...
Twitter:
gabrielylr
Scholar ID:
Google Scholar Page
Last seen:
4 hours ago
Joined:
7 years, 6 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 • 361 results • page 1 of 37 • next >
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Comment: C: bcl2fastq with xGen Dual Index UMI Adapters to produce 3 read and 2 index fastqs
... Could you post a few sequences and a mini diagram of what you expect like [Adapter] [UMI] [SEQ] .. ? ...
written 25 days ago by Gabriel R.2.6k
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Comment: C: Merging unaligned bam files
... What is wrong with samtools cat? ...
written 4 weeks ago by Gabriel R.2.6k
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Answer: A: Allele count from BAM file
... It is one line in [glactools][1]: glactools bam2acf [reference].fa [iinput].bam sampleid | glactools view - |cut -f 1-3,6 In the last column, the format is REF,ALT:cpg Be aware that it filters out reads marked as QC failed and PCR duplicates. [1]: https://grenaud.github.io/glactools/ ...
written 8 weeks ago by Gabriel R.2.6k
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Answer: A: Convert vcf phased data to plink
... You can try [glactools][1], it is just one line: glactools vcfm2acf --onlyGT --fai /Data/reference/human_g1k_v37.fasta.fai /tmp/biostars/test.vcf | glactools acf2bplink - /tmp/biostars/test You need to edit the genetic distance in the bim file and probably the fam files as well. [1]: h ...
written 3 months ago by Gabriel R.2.6k
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Comment: C: How to find out human mtDNA genes in d-loop control region for Indian origin onl
... But there are many different haplotypes in India. What do you mean Indian origin? ...
written 3 months ago by Gabriel R.2.6k
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Comment: C: Demultiplexing and deduplicating using barcodes and UMIs in the "mate" read
... if you have dedicate cycles, it's ok, I was wondering about the output format. ...
written 4 months ago by Gabriel R.2.6k
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Comment: C: Demultiplexing and deduplicating using barcodes and UMIs in the "mate" read
... I don't get it. You will simply prime next to read2 and hope to run into the barcode+UMI? ...
written 4 months ago by Gabriel R.2.6k
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Comment: C: Demultiplexing and deduplicating using barcodes and UMIs in the "mate" read
... But that is assuming the adapters were sequenced. Were there sequencing cycles to sequence the indices? ...
written 4 months ago by Gabriel R.2.6k
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Comment: C: Demultiplexing and deduplicating using barcodes and UMIs in the "mate" read
... Could you post a few lines as example? Do you have an index list? ...
written 4 months ago by Gabriel R.2.6k
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Comment: C: ANGSD vs GATK for genotype likelihoods
... I am not 100% sure but ANGSD only implements the error model in GATK with "-gl 2" and the samtools one with "-gl 1" ...
written 4 months ago by Gabriel R.2.6k

Latest awards to Gabriel R.

Popular Question 6 months ago, created a question with more than 1,000 views. For Merge Scaffolds From Different Individuals?
Scholar 7 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
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
Good Answer 11 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 11 months ago, created a question with more than 1,000 views. For Psmc Parameters To Use
Teacher 12 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 12 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 12 months ago, created a question with more than 5,000 views. For Out Of Disk Space With Picard Tools ?
Scholar 14 months ago, created an answer that has been accepted. For A: Evolutionary distance models
Scholar 18 months ago, created an answer that has been accepted. For A: Evolutionary distance models
Appreciated 19 months ago, created a post with more than 5 votes. For C: gender SNP marker
Popular Question 19 months ago, created a question with more than 1,000 views. For Raxml (Residues Read In Sequence)
Popular Question 19 months ago, created a question with more than 1,000 views. For Create A Consensus Of Very Short Sequences
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 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 23 months 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
Scholar 2.0 years ago, created an answer that has been accepted. For A: Evolutionary distance models
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
Scholar 2.1 years ago, created an answer that has been accepted. For A: Evolutionary distance models
Good Answer 2.1 years ago, created an answer that was upvoted at least 5 times. For A: What Software Programs Do Bioinformaticians Need?
Student 2.2 years ago, asked a question with at least 3 up-votes. For Out Of Disk Space With Picard Tools ?
Popular Question 2.4 years ago, created a question with more than 1,000 views. For Merge Scaffolds From Different Individuals?
Epic Question 2.4 years ago, created a question with more than 10,000 views. For Out Of Disk Space With Picard Tools ?

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