User: Gabriel R.

gravatar for Gabriel R.
Gabriel R.2.6k
Reputation:
2,570
Status:
Trusted
Location:
Center for Geogenetik Københavns Universitet
Website:
https://grenaud.github...
Twitter:
gabrielylr
Scholar ID:
Google Scholar Page
Last seen:
13 hours ago
Joined:
7 years, 2 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 • 356 results • page 1 of 36 • next >
0
votes
1
answer
158
views
1
answers
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 22 days ago by Gabriel R.2.6k
0
votes
1
answer
158
views
1
answers
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 23 days ago by Gabriel R.2.6k
0
votes
1
answer
158
views
1
answers
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 25 days ago by Gabriel R.2.6k
0
votes
1
answer
158
views
1
answers
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 26 days ago by Gabriel R.2.6k
0
votes
0
answers
95
views
0
answers
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 5 weeks ago by Gabriel R.2.6k
0
votes
1
answer
132
views
1
answers
Comment: C: deML: ERROR: Discrepancy between fastq files, different names with first index
... They should have the same names as your forward reads, in your case: "M04129:63:000000000-D656Y:1:1101:15821:1334" ...
written 8 weeks ago by Gabriel R.2.6k
0
votes
1
answer
132
views
1
answers
Answer: A: deML: ERROR: Discrepancy between fastq files, different names with first index
... This indicates that the defline for the forward read and the first index are not the same. You have a record with a defline "@F1". Are you sure this is the per read index? Could you perhaps post the first 40 lines of both files? ...
written 8 weeks ago by Gabriel R.2.6k
0
votes
2
answers
309
views
2
answers
Answer: A: Problem with demultiplexing illumina dual indexed libraries
... I am biased but I would recommend my own [deML][1]. It is a maximum-likelihood demultiplexer which is designed to deal with uncertainty and partial information. I still maintain it, let me know if you have any issues. [1]: http://grenaud.github.io/deML/ ...
written 11 weeks ago by Gabriel R.2.6k
1
vote
1
answer
326
views
1
answers
Answer: A: Error when using deML with dual indexed paired end sequencs
... Hi both, those are just warnings. deML (http://grenaud.github.io/deML/) is robust to poorly designed indices lists or sequencing runs with very poor quality. These warnings just inform you that an index was used. I have since added this to the README, let me know if this is sufficiently clear and ve ...
written 3 months ago by Gabriel R.2.6k
0
votes
0
answers
196
views
0
answers
Comment: C: combining phylogenetic trees into a consensus super Tree
... have you tried cegg.unige.ch/newick_utils ? what does it produce? ...
written 3 months ago by Gabriel R.2.6k

Latest awards to Gabriel R.

Popular Question 10 weeks ago, created a question with more than 1,000 views. For Merge Scaffolds From Different Individuals?
Scholar 3 months ago, created an answer that has been accepted. For A: Evolutionary distance models
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
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 7 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 7 months ago, created a question with more than 1,000 views. For Psmc Parameters To Use
Teacher 8 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 8 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 8 months ago, created a question with more than 5,000 views. For Out Of Disk Space With Picard Tools ?
Scholar 10 months ago, created an answer that has been accepted. For A: Evolutionary distance models
Scholar 14 months ago, created an answer that has been accepted. For A: Evolutionary distance models
Appreciated 15 months ago, created a post with more than 5 votes. For C: gender SNP marker
Popular Question 15 months ago, created a question with more than 1,000 views. For Raxml (Residues Read In Sequence)
Popular Question 15 months ago, created a question with more than 1,000 views. For Create A Consensus Of Very Short Sequences
Teacher 16 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 20 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 20 months ago, created an answer that has been accepted. For A: Evolutionary distance models
Appreciated 20 months ago, created a post with more than 5 votes. For C: gender SNP marker
Scholar 20 months ago, created an answer that has been accepted. For A: Evolutionary distance models
Teacher 20 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 22 months ago, created an answer that has been accepted. For A: Evolutionary distance models
Good Answer 22 months ago, created an answer that was upvoted at least 5 times. For A: What Software Programs Do Bioinformaticians Need?
Student 23 months ago, asked a question with at least 3 up-votes. For Out Of Disk Space With Picard Tools ?
Popular Question 2.1 years ago, created a question with more than 1,000 views. For Merge Scaffolds From Different Individuals?
Epic Question 2.1 years ago, created a question with more than 10,000 views. For Out Of Disk Space With Picard Tools ?

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1659 users visited in the last hour