User: Gabriel R.

gravatar for Gabriel R.
Gabriel R.2.2k
Reputation:
2,220
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:
5 years, 9 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 • 294 results • page 1 of 30 • next >
0
votes
1
answer
340
views
1
answers
Comment: C: Converting ms or msms output to PLINK or VCF files
... another comment, I do not know what you are trying to do but the ms output produces this output under an infinite sites model and these represent mutations occurring in different branches in the tree. To quote the manual: "An infinite sites model of mutation is assumed, and thus multiple-hits and ba ...
written 6 days ago by Gabriel R.2.2k
0
votes
1
answer
340
views
1
answers
Comment: C: Converting ms or msms output to PLINK or VCF files
... This is a tangent but I really like msprime as it can give you VCF format directly. ...
written 7 days ago by Gabriel R.2.2k
3
votes
0
answers
115
views
0
answers
Tool: glactools: command-line tools for the management of genotype likelihoods and allele counts
... Hello biostars! I coded this set of programs to help groups dealing with genotypes/variant data/allele counts and need to store, analyze, filter and export that data to various formats used by pop. gen. software. It used bgzipped/binary files designed to store genotype likelihoods or allele counts. ...
population genetics tool variants written 5 weeks ago by Gabriel R.2.2k
0
votes
2
answers
211
views
2
answers
Comment: C: Split BAM file from more sample
... the program creates one file per RG in the header, can you do an 'ls -al' in your directory? ...
written 5 weeks ago by Gabriel R.2.2k
0
votes
2
answers
211
views
2
answers
Comment: C: Split BAM file from more sample
... Then the program I mentioned should work and give you 1 bam file per sample while going through the bam file once. ...
written 5 weeks ago by Gabriel R.2.2k
0
votes
2
answers
211
views
2
answers
Comment: C: Split BAM file from more sample
... ok, so for this read, the read group is l7izc? How come rg is not capitalized? How was demultiplexing done? ...
written 5 weeks ago by Gabriel R.2.2k
0
votes
2
answers
211
views
2
answers
Comment: C: Split BAM file from more sample
... could you do a samtools view input.bam |head -1 and post the results? ...
written 5 weeks ago by Gabriel R.2.2k
0
votes
1
answer
184
views
1
answers
Comment: C: How can I restore paired-end fastq files from a sorted bam file with fastq remai
... Ok, what about reads getting assigned to random positions due to poor mapping quality, they will not end up in the same position? And to re-iterate my initial question, may I ask why you need this? ...
written 5 weeks ago by Gabriel R.2.2k
0
votes
2
answers
211
views
2
answers
Answer: A: Split BAM file from more sample
... if you want one bam file per sample and have RG tags, you can use my little program here: https://github.com/grenaud/libbam/blob/master/splitByRG.cpp otherwise, you can just iterate over each RG using samtools view -r [rg] but then you go over each record 11 times. ...
written 6 weeks ago by Gabriel R.2.2k
0
votes
1
answer
184
views
1
answers
Comment: C: How can I restore paired-end fastq files from a sorted bam file with fastq remai
... May I ask why you need this? ...
written 6 weeks ago by Gabriel R.2.2k

Latest awards to Gabriel R.

Teacher 11 weeks ago, created an answer with at least 3 up-votes. For A: How To Interpret The Kmer Enrichment Plot Of A Fastqc Output
Scholar 11 weeks ago, created an answer that has been accepted. For A: Evolutionary distance models
Appreciated 3 months ago, created a post with more than 5 votes. For C: gender SNP marker
Scholar 3 months ago, created an answer that has been accepted. For A: Evolutionary distance models
Teacher 3 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 4 months ago, created an answer that has been accepted. For A: Evolutionary distance models
Good Answer 4 months ago, created an answer that was upvoted at least 5 times. For A: What Software Programs Do Bioinformaticians Need?
Student 5 months ago, asked a question with at least 3 up-votes. For Out Of Disk Space With Picard Tools ?
Popular Question 7 months ago, created a question with more than 1,000 views. For Merge Scaffolds From Different Individuals?
Epic Question 8 months ago, created a question with more than 10,000 views. For Out Of Disk Space With Picard Tools ?
Good Question 11 months ago, asked a question that was upvoted at least 5 times. For Out Of Disk Space With Picard Tools ?
Popular Question 14 months ago, created a question with more than 1,000 views. For Duplicate Removal Of New Sequence Data?
Popular Question 16 months ago, created a question with more than 1,000 views. For Chry In 1000G Vs Hg19
Scholar 17 months ago, created an answer that has been accepted. For A: Evolutionary distance models
Appreciated 17 months ago, created a post with more than 5 votes. For C: gender SNP marker
Teacher 17 months ago, created an answer with at least 3 up-votes. For A: How To Write A Perl Script To Transform A Sequence In A Tabular File Into A Fast
Voter 18 months ago, voted more than 100 times.
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 A: Should I Do A Dual Master Degree In Both Bioinformatics And Cs?
Teacher 19 months ago, created an answer with at least 3 up-votes. For A: How To Write A Perl Script To Transform A Sequence In A Tabular File Into A Fast
Good Answer 19 months ago, created an answer that was upvoted at least 5 times. For A: What Software Programs Do Bioinformaticians Need?
Teacher 19 months ago, created an answer with at least 3 up-votes. For A: How To Write A Perl Script To Transform A Sequence In A Tabular File Into A Fast
Scholar 21 months ago, created an answer that has been accepted. For A: Evolutionary distance models
Popular Question 21 months ago, created a question with more than 1,000 views. For Iupac Bases In The Hg19 1000G Reference ?
Appreciated 21 months ago, created a post with more than 5 votes. For A: Programming Language In Bioinformatics

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1174 users visited in the last hour