User: Gabriel R.

gravatar for Gabriel R.
Gabriel R.2.1k
Reputation:
2,070
Status:
Trusted
Location:
Center for Geogenetik Københavns Universitet
Website:
https://grenaud.github...
Twitter:
gabrielylr
Scholar ID:
Google Scholar Page
Last seen:
14 minutes ago
Joined:
5 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 • 264 results • page 1 of 27 • next >
0
votes
1
answer
137
views
1
answers
Answer: A: Are there any tools to simulate mutations?
... msprime (https://github.com/jeromekelleher/msprime). You can simulate a demography of say 10 individuals and output segregating sites as VCF. You can even plug in a recombination map. ...
written 11 hours ago by Gabriel R.2.1k
0
votes
1
answer
139
views
1
answers
Comment: C: How to Demultiplex dual indexed Illumina reads
... could you post an example of what your data looks like? ...
written 11 days ago by Gabriel R.2.1k
5
votes
1
answer
111
views
1
answers
Answer: A: Do I need to merge bai files also, while merging bam files
... do samtools index merged_filename.bam ...
written 11 days ago by Gabriel R.2.1k
0
votes
2
answers
212
views
2
answers
Comment: C: Which approaches and/or tools for detection and removal of contaminants?
... Could you refine your question, what do you mean by "contaminants"? ...
written 6 weeks ago by Gabriel R.2.1k
0
votes
2
answers
980
views
2
answers
Answer: A: simulating illumina data with spiked variants
... For 1, 2 (maybe 3), 4 we developed a sequencing simulator for ancient DNA: [grenaud.github.io/gargammel/][1] But it can be used to simulate modern DNA. For the PhiX, you can add it as a "microbial contaminant". It automates the process of fragment size distribution, sampling from a diploid genome a ...
written 7 weeks ago by Gabriel R.2.1k
2
votes
4
answers
645
views
4
answers
Answer: A: weird insert size post trimming
... If you try leeHom ([https://grenaud.github.io/leeHom/][1]), it can trim adapters and merge overlapping using a Bayesian algorithm so no cutoffs are required. It will produce 3 types of files to map: 1. [PREFIX].fq.gz Sequences that were trimmed and merged confidently by leeHom 2. [PREFIX]_r1.fq.g ...
written 8 weeks ago by Gabriel R.2.1k
0
votes
4
answers
645
views
4
answers
Comment: C: weird insert size post trimming
... sure my gmail: gabriel [dot here] reno ...
written 8 weeks ago by Gabriel R.2.1k
0
votes
4
answers
645
views
4
answers
Comment: C: weird insert size post trimming
... get pysam and run: python insertSize.py in.bam #!/usr/bin/python import pysam import sys; bamInputFile = pysam.Samfile(sys.argv[1], "rb"); for read in bamInputFile: if read.is_unmapped : continue; if read.is_paired : ...
written 8 weeks ago by Gabriel R.2.1k
0
votes
4
answers
645
views
4
answers
Comment: C: weird insert size post trimming
... how about: samtools view mapped.bam |awk 'function abs(x){return ((x < 0.0) ? -x : x)} {if(and($2,5)==0){print length($10);}else{ if(and($2,66)==66){ print abs($9); }} }' ...
written 8 weeks ago by Gabriel R.2.1k • updated 8 weeks ago by genomax34k
0
votes
4
answers
645
views
4
answers
Comment: C: weird insert size post trimming
... because the reads with less than 126 bp are found there. ...
written 8 weeks ago by Gabriel R.2.1k

Latest awards to Gabriel R.

Appreciated 11 days ago, created a post with more than 5 votes. For C: gender SNP marker
Teacher 11 days 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 days ago, created an answer that has been accepted. For A: Evolutionary distance models
Scholar 8 weeks ago, created an answer that has been accepted. For A: Evolutionary distance models
Good Answer 8 weeks ago, created an answer that was upvoted at least 5 times. For A: What Software Programs Do Bioinformaticians Need?
Student 11 weeks ago, asked a question with at least 3 up-votes. For Out Of Disk Space With Picard Tools ?
Popular Question 5 months ago, created a question with more than 1,000 views. For Merge Scaffolds From Different Individuals?
Epic Question 5 months ago, created a question with more than 10,000 views. For Out Of Disk Space With Picard Tools ?
Good Question 8 months ago, asked a question that was upvoted at least 5 times. For Out Of Disk Space With Picard Tools ?
Popular Question 11 months ago, created a question with more than 1,000 views. For Duplicate Removal Of New Sequence Data?
Popular Question 13 months ago, created a question with more than 1,000 views. For Chry In 1000G Vs Hg19
Appreciated 14 months ago, created a post with more than 5 votes. For C: gender SNP marker
Scholar 14 months ago, created an answer that has been accepted. For A: Evolutionary distance models
Teacher 14 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 15 months ago, voted more than 100 times.
Scholar 16 months ago, created an answer that has been accepted. For A: Evolutionary distance models
Appreciated 16 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 16 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 16 months ago, created an answer that was upvoted at least 5 times. For A: What Software Programs Do Bioinformaticians Need?
Teacher 16 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 18 months ago, created an answer that has been accepted. For A: Evolutionary distance models
Popular Question 18 months ago, created a question with more than 1,000 views. For Iupac Bases In The Hg19 1000G Reference ?
Appreciated 18 months ago, created a post with more than 5 votes. For A: Programming Language In Bioinformatics
Popular Question 2.0 years ago, created a question with more than 1,000 views. For Duplicate Removal Of New Sequence Data?
Appreciated 2.2 years 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: 1383 users visited in the last hour