Moderator: Manu Prestat

gravatar for Manu Prestat
Manu Prestat3.8k
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Location:
Marseille, France
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http://www.prestat.fr/
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ManuFrenchy
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Check out my blog here: http://exploringlifedata.blogspot.com/

Posts by Manu Prestat

<prev • 327 results • page 1 of 33 • next >
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Answer: A: Getting BLAST to give output whilst running
... Some answers here: https://www.biostars.org/p/16471/ ...
written 17 days ago by Manu Prestat3.8k
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Comment: C: Parsing the NR database
... Metazoa (Taxonomy ID: 33208) could be a good candidate for "animals". ...
written 10 weeks ago by Manu Prestat3.8k
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Answer: A: Metagenomics functional annotation hmmsearch vs Blast ???
... There is also this hmm db: http://cbb.pnnl.gov/portal/software/FOAM.html (for which, I should say, I was a bit involved). ...
written 3 months ago by Manu Prestat3.8k
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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 11 months ago by Manu Prestat3.8k
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Comment: C: Software for viewing very large data
... or zcat ;-) ...
written 11 months ago by Manu Prestat3.8k
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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 11 months ago by Manu Prestat3.8k
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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 11 months ago by Manu Prestat3.8k
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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 12 months ago by Manu Prestat3.8k • updated 12 months ago by i.sudbery1.4k
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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 14 months ago by Manu Prestat3.8k
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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 14 months ago by Manu Prestat3.8k

Latest awards to Manu Prestat

Appreciated 9 weeks ago, created a post with more than 5 votes. For C: Single Gene Orthologs
Good Answer 12 weeks ago, created an answer that was upvoted at least 5 times. For A: Pyfasta Split By Header
Great Question 3 months ago, created a question with more than 5,000 views. For How To Concatenate/Merge Blast Xml Outputs?
Popular Question 10 months ago, created a question with more than 1,000 views. For Estimation Of The Probability Of Chimera In A Metagenomic Assembly?
Teacher 11 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 11 months ago, created a post with more than 10 bookmarks. For Best bioinfo one-liners?
Appreciated 11 months ago, created a post with more than 5 votes. For C: Single Gene Orthologs
Scholar 13 months ago, created an answer that has been accepted. For A: Show Progress (Bar?) For Blast+ Query
Teacher 13 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 13 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 14 months ago, created a comment with at least 3 up-votes. For C: Transition/Transversion Ratio From Fastq Files
Good Answer 16 months ago, created an answer that was upvoted at least 5 times. For A: Calculating P-Values From Z-Scores
Scholar 16 months ago, created an answer that has been accepted. For A: Show Progress (Bar?) For Blast+ Query
Popular Question 16 months ago, created a question with more than 1,000 views. For How To Filter A Blast Xml Output ?
Appreciated 18 months ago, created a post with more than 5 votes. For C: Single Gene Orthologs
Popular Question 18 months ago, created a question with more than 1,000 views. For How To Filter A Blast Xml Output ?
Good Answer 20 months ago, created an answer that was upvoted at least 5 times. For A: Calculating P-Values From Z-Scores
Popular Question 22 months ago, created a question with more than 1,000 views. For Sanger Paired-End Assembly
Popular Question 22 months ago, created a question with more than 1,000 views. For Sanger Paired-End Assembly
Appreciated 24 months ago, created a post with more than 5 votes. For C: Single Gene Orthologs
Popular Question 2.2 years ago, created a question with more than 1,000 views. For Sanger Paired-End Assembly
Teacher 2.2 years 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 2.3 years ago, created a post with more than 20 followers. For Best bioinfo one-liners?
Good Question 2.3 years ago, asked a question that was upvoted at least 5 times. For Best bioinfo one-liners?
Appreciated 2.3 years ago, created a post with more than 5 votes. For C: Single Gene Orthologs

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