User: 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.
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... 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
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139
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... could you post an example of what your data looks like? ...
written 11 days ago by
Gabriel R. • 2.1k
5
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1
answer
111
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1
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... do
samtools index merged_filename.bam ...
written 11 days ago by
Gabriel R. • 2.1k
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2
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212
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... Could you refine your question, what do you mean by "contaminants"? ...
written 6 weeks ago by
Gabriel R. • 2.1k
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2
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... 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
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... 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
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4
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645
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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
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4
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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
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645
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4
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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
genomax ♦ 34k
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.
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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
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8 weeks ago,
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For A: What Software Programs Do Bioinformaticians Need?
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For Out Of Disk Space With Picard Tools ?
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5 months ago,
created a question with more than 1,000 views.
For Merge Scaffolds From Different Individuals?
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created a question with more than 10,000 views.
For Out Of Disk Space With Picard Tools ?
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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?
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13 months ago,
created a question with more than 1,000 views.
For Chry In 1000G Vs Hg19
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14 months ago,
created an answer that has been accepted.
For A: Evolutionary distance models
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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
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16 months ago,
created an answer that has been accepted.
For A: Evolutionary distance models
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created a post with more than 5 votes.
For A: Should I Do A Dual Master Degree In Both Bioinformatics And Cs?
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16 months ago,
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For A: How To Write A Perl Script To Transform A Sequence In A Tabular File Into A Fast
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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 ?
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For A: Programming Language In Bioinformatics
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For Duplicate Removal Of New Sequence Data?
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2.2 years ago,
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For A: Programming Language In Bioinformatics
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