Moderator: Manu Prestat

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

Posts by Manu Prestat

<prev • 328 results • page 1 of 33 • next >
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Comment: C: Split fasta/fastq into individual fasta files (ubuntu)
... Of course, it should not be a nightmare to write a script that takes a fastq file in input, and deliver per-read fasta files in output. An issue you may encounter, depending on your filesystem I guess, is the number of inodes management. An idea could be to separate the fasta files into different fo ...
written 24 days ago by Manu Prestat3.8k
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Answer: A: Getting BLAST to give output whilst running
... Some answers here: https://www.biostars.org/p/16471/ ...
written 11 weeks 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 4 months 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 5 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 13 months ago by Manu Prestat3.8k
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Comment: C: Software for viewing very large data
... or zcat ;-) ...
written 13 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 13 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 13 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 14 months ago by Manu Prestat3.8k • updated 14 months ago by i.sudbery1.6k
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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 16 months ago by Manu Prestat3.8k

Latest awards to Manu Prestat

Appreciated 4 months ago, created a post with more than 5 votes. For C: Single Gene Orthologs
Good Answer 5 months ago, created an answer that was upvoted at least 5 times. For A: Pyfasta Split By Header
Great Question 5 months ago, created a question with more than 5,000 views. For How To Concatenate/Merge Blast Xml Outputs?
Popular Question 12 months ago, created a question with more than 1,000 views. For Estimation Of The Probability Of Chimera In A Metagenomic Assembly?
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?
Librarian 13 months ago, created a post with more than 10 bookmarks. For Best bioinfo one-liners?
Appreciated 13 months ago, created a post with more than 5 votes. For C: Single Gene Orthologs
Scholar 15 months ago, created an answer that has been accepted. For A: Show Progress (Bar?) For Blast+ Query
Teacher 15 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 15 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 17 months ago, created a comment with at least 3 up-votes. For C: Transition/Transversion Ratio From Fastq Files
Good Answer 18 months ago, created an answer that was upvoted at least 5 times. For A: Calculating P-Values From Z-Scores
Scholar 18 months ago, created an answer that has been accepted. For A: Show Progress (Bar?) For Blast+ Query
Popular Question 18 months ago, created a question with more than 1,000 views. For How To Filter A Blast Xml Output ?
Appreciated 20 months ago, created a post with more than 5 votes. For C: Single Gene Orthologs
Popular Question 20 months ago, created a question with more than 1,000 views. For How To Filter A Blast Xml Output ?
Good Answer 22 months ago, created an answer that was upvoted at least 5 times. For A: Calculating P-Values From Z-Scores
Popular Question 2.0 years ago, created a question with more than 1,000 views. For Sanger Paired-End Assembly
Popular Question 2.0 years ago, created a question with more than 1,000 views. For Sanger Paired-End Assembly
Appreciated 2.2 years ago, created a post with more than 5 votes. For C: Single Gene Orthologs
Popular Question 2.3 years ago, created a question with more than 1,000 views. For Sanger Paired-End Assembly
Teacher 2.4 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 2.4 years ago, created a post with more than 20 followers. For Best bioinfo one-liners?
Good Question 2.4 years ago, asked a question that was upvoted at least 5 times. For Best bioinfo one-liners?
Appreciated 2.4 years ago, created a post with more than 5 votes. For C: Single Gene Orthologs

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