Moderator: Manu Prestat

gravatar for Manu Prestat
Manu Prestat3.7k
Reputation:
3,680
Status:
Trusted
Location:
Marseille, France
Website:
http://www.prestat.fr/
Twitter:
ManuFrenchy
Scholar ID:
Google Scholar Page
Last seen:
2 days, 20 hours ago
Joined:
4 years, 9 months ago
Email:
e*******************@gmail.com

Check out my blog here: http://exploringlifedata.blogspot.com/

Posts by Manu Prestat

<prev • 324 results • page 1 of 33 • next >
0
votes
3
answers
275
views
3
answers
Comment: C: Color Triangle and plot
... Hi, well, here I've just randomly generated 400 values between 0 and 1 (such as your triangle example) for A, B and C. Instead, I believe you would make a matrix with B,C,A as columns (to be in the same order as RGB in your example), and your measurements as rows. And then you plot with pixmapRGB() ...
written 4 months ago by Manu Prestat3.7k
0
votes
1
answer
277
views
1
answers
Comment: C: Software for viewing very large data
... or zcat ;-) ...
written 4 months ago by Manu Prestat3.7k
1
vote
3
answers
275
views
3
answers
Answer: A: Color Triangle and plot
... What about pixmapRGB() ? library(pixmap) A <- runif(n = 400, min = 0, max = 1) B <- runif(n = 400, min = 0, max = 1) C <- runif(n = 400, min = 0, max = 1) z <- pixmapRGB(c(B,C,A), 20, 20, bbox=c(-1,-1,1,1)) plot(z) ...
written 4 months ago by Manu Prestat3.7k
1
vote
1
answer
265
views
1
answers
Answer: A: How to extract chrX, chrY and chrM from a vcf file?
... Using vcftools you could pass the chromosomes you want to keep (or exclude) with the position filtering option: POSITION FILTERING --chr --not-chr Includes or excludes sites with indentifiers matching . These options may be used multiple times to include or exclude more ...
written 4 months ago by Manu Prestat3.7k
0
votes
1
answer
243
views
1
answer
Sequences with molecular indexes processing
... Hi, I have some sequencing files which include 8nt molecular indexes on both ends. So I remove them before mapping to the genome, and now I would like to deduplicate the reads with same molecular indexes. I found https://github.com/mbusby/AddUMIsToBam but not sure it is maintained and properly teste ...
ngs written 5 months ago by Manu Prestat3.7k • updated 5 months ago by i.sudbery970
1
vote
3
answers
264
views
3
answers
Answer: A: What is local maximum in sequence alignments ?
... Often, heuristic algorithms are driven by an optimization function, e.g. looking for the minimization of the penalty score for an alignment. If the algorithm does not guaranty the "global" minimum score, it means that the minimum found can be a "local" minimum. Thus, the best solution (in this case ...
written 7 months ago by Manu Prestat3.7k
0
votes
0
answers
211
views
0
answers
Review mRNA primer pairs positions on genome assembly
... Dear forum, I would like to review a set of ~ 50 human RNA primer pairs (in fasta) on a genome browser. Their size range from 18 to 25nt. Some of them overlap splicing junctions. I have tried two approaches: 1. blast on refseq RNA: fine but need a conversion to grch37 assembly (allowing split ...
sequence written 7 months ago by Manu Prestat3.7k
1
vote
13
answers
2.8k
views
13
answers
Comment: C: Good Habit for Bioinformatics Analyst or Scientist
... OK but don't think less! ...
written 8 months ago by Manu Prestat3.7k
0
votes
4
answers
856
views
4
answers
Answer: A: Is there an alternative to Cytoscape software for building graphs from microarra
... [ggnet2][1] a network visualization with [ggplot2][2] (for R). [1]: https://briatte.github.io/ggnet/ [2]: http://ggplot2.org/ ...
written 8 months ago by Manu Prestat3.7k
0
votes
2
answers
276
views
2
answers
Answer: A: what's the difference between mapping PE fastqs to genome and to specified targe
... Option 1: whole genome mapping is obviously slower, but it is more accurate as the reads will map onto the most similar region it finds. Option 2: a way faster, but may provide wrong results (*i.e.* reads of a sequence originated from an other part of the genome). It really depends on how was desi ...
written 9 months ago by Manu Prestat3.7k

Latest awards to Manu Prestat

Popular Question 3 months ago, created a question with more than 1,000 views. For Estimation Of The Probability Of Chimera In A Metagenomic Assembly?
Teacher 4 months ago, created an answer with at least 3 up-votes. For A: Are We Rude/Do We Expect Too Much From People Asking Questions On This Forum?
Librarian 4 months ago, created a post with more than 10 bookmarks. For Best bioinfo one-liners?
Appreciated 4 months ago, created a post with more than 5 votes. For C: Single Gene Orthologs
Scholar 6 months ago, created an answer that has been accepted. For A: Show Progress (Bar?) For Blast+ Query
Teacher 6 months ago, created an answer with at least 3 up-votes. For A: Are We Rude/Do We Expect Too Much From People Asking Questions On This Forum?
Teacher 6 months ago, created an answer with at least 3 up-votes. For A: Are We Rude/Do We Expect Too Much From People Asking Questions On This Forum?
Commentator 8 months ago, created a comment with at least 3 up-votes. For C: Transition/Transversion Ratio From Fastq Files
Scholar 9 months ago, created an answer that has been accepted. For A: Show Progress (Bar?) For Blast+ Query
Good Answer 9 months ago, created an answer that was upvoted at least 5 times. For A: Calculating P-Values From Z-Scores
Popular Question 9 months ago, created a question with more than 1,000 views. For How To Filter A Blast Xml Output ?
Appreciated 11 months ago, created a post with more than 5 votes. For C: Single Gene Orthologs
Popular Question 11 months ago, created a question with more than 1,000 views. For How To Filter A Blast Xml Output ?
Good Answer 13 months ago, created an answer that was upvoted at least 5 times. For A: Calculating P-Values From Z-Scores
Popular Question 15 months ago, created a question with more than 1,000 views. For Sanger Paired-End Assembly
Popular Question 15 months ago, created a question with more than 1,000 views. For Sanger Paired-End Assembly
Appreciated 17 months ago, created a post with more than 5 votes. For C: Single Gene Orthologs
Popular Question 19 months ago, created a question with more than 1,000 views. For Sanger Paired-End Assembly
Teacher 19 months ago, created an answer with at least 3 up-votes. For A: Are We Rude/Do We Expect Too Much From People Asking Questions On This Forum?
Prophet 20 months ago, created a post with more than 20 followers. For Best bioinfo one-liners?
Good Question 20 months ago, asked a question that was upvoted at least 5 times. For Best bioinfo one-liners?
Appreciated 20 months ago, created a post with more than 5 votes. For C: Single Gene Orthologs
Student 20 months ago, asked a question with at least 3 up-votes. For Estimation Of The Probability Of Chimera In A Metagenomic Assembly?
Good Answer 20 months ago, created an answer that was upvoted at least 5 times. For A: What Are The Most Common Stupid Mistakes In Bioinformatics?
Good Answer 20 months ago, created an answer that was upvoted at least 5 times. For A: What Are The Most Common Stupid Mistakes 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: 1226 users visited in the last hour