Moderator: Eric Normandeau

gravatar for Eric Normandeau
Eric Normandeau9.1k
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Location:
Quebec, Canada
Website:
http://github.com/enor...
Last seen:
3 weeks ago
Joined:
6 years, 9 months ago
Email:
e**************@hotmail.com
  • Biologist turned bioinformatician, fluent in Python, R, and bash, now learning C

  • I have worked with microarrays, qRT-PCR and am currently working with RAD sequencing, Genotyping by Sequencing, and RNA-Seq.

  • If you are new to biostar, you can read the following: How to ask Good Questions on Technical and Scientific Forums

Posts by Eric Normandeau

<prev • 638 results • page 1 of 64 • next >
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Comment: C: writing bash script with python
... I did wanted to close originally but I didn't. We'll see if a new question by OP will come up. ...
written 12 weeks ago by Eric Normandeau9.1k
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Comment: C: writing bash script with python
... If I get you correctly, you are trying to create a high number of job submission scripts for a server. This is probably a bad approach. You probably need one script that treats all your fastq files, ideally in parallel on a certain number of CPUs. Please, do consider posting a new question where you ...
written 12 weeks ago by Eric Normandeau9.1k
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Comment: C: writing bash script with python
... I think you are right. Suggesting a new, better formed question but this question should be deleted IMO. ...
written 12 weeks ago by Eric Normandeau9.1k
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Comment: C: writing bash script with python
... Your question really is unclear. We need more information to be able to help you. Please take the time to clarify your question and post a new one that clearly states what you are trying to accomplish, how, and what seems to not work. Please take the time to read this before posting your new questi ...
written 12 weeks ago by Eric Normandeau9.1k
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Comment: C: Combining The Paired Reads From Illumina Run
... The script was written for Python 2.7. There is a possibility it will not work if you are using Python 3.x the server. You can test this with `which python`. ...
written 3 months ago by Eric Normandeau9.1k
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Comment: C: [UPDATE] Thrown into a Bioinformatics Position
... > In the end, is bioinformatics more fun than World of Warcraft? :-) That is the real question :) ...
written 7 months ago by Eric Normandeau9.1k
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Comment: C: Eukaryotic Genome Annotation in 2016
... We finished step 5 and are wondering how you extracted your list of "high-confidence" gene predictions in step 6. The EVM output and gff3 output are fairly different in terms of what information they present. Eg: the evidence provenances are only found in the output but are not found in the gff3 out ...
written 8 months ago by Eric Normandeau9.1k
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Comment: C: Eukaryotic Genome Annotation in 2016
... Thanks for the `exonerate` help! We are now at the `snap` stage. Our species is quite close to *Drosophila melanogaster*, for which an `.hmm` file is provided. Do you think we need to train `snap` with our specific genome? I guess using the `D.melanogaster.hmm` should be OK? Did you have to train `s ...
written 9 months ago by Eric Normandeau9.1k
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Comment: C: Eukaryotic Genome Annotation in 2016
... By `I only kept hits where at least 50% of the protein aligns`, to you mean you used `--percent 50`? If yes, that is not exactly what the `--percent` option does. It keeps proteins for which the actual score is at least 50% of the maximum possible score, which is a bit different given how the score ...
written 9 months ago by Eric Normandeau9.1k
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Comment: C: Eukaryotic Genome Annotation in 2016
... We are running `exonerate` now and are playing with the parameters, which can have a tremendous impact on the number hits (from very few to crazy high hits). What parameters did you use in your annotation? ...
written 9 months ago by Eric Normandeau9.1k

Latest awards to Eric Normandeau

Appreciated 5 weeks ago, created a post with more than 5 votes. For A: Python 2 Vs Python 3 In Bioinformatics
Great Question 12 weeks ago, created a question with more than 5,000 views. For Code Golf: Mean Length Of Fasta Sequences
Great Question 12 weeks ago, created a question with more than 5,000 views. For Snp Detection And Genotyping In Ngs (Next Generation Sequencing)
Teacher 12 weeks ago, created an answer with at least 3 up-votes. For A: Python 2 Vs Python 3 In Bioinformatics
Student 12 weeks ago, asked a question with at least 3 up-votes. For Automate High-Volume Sequence Annotation And Genbank Submission
Popular Question 3 months ago, created a question with more than 1,000 views. For Automate High-Volume Sequence Annotation And Genbank Submission
Good Question 4 months ago, asked a question that was upvoted at least 5 times. For Post Your Prefered Bioinformatics Short Code
Pundit 4 months ago, created a comment with more than 10 votes. For C: Multiline Fasta To Single Line Fasta
Popular Question 4 months ago, created a question with more than 1,000 views. For Automate High-Volume Sequence Annotation And Genbank Submission
Commentator 5 months ago, created a comment with at least 3 up-votes. For C: Biology Introduction For A Computer Scientist
Great Question 6 months ago, created a question with more than 5,000 views. For Code Golf: Mean Length Of Fasta Sequences
Student 6 months ago, asked a question with at least 3 up-votes. For Automate High-Volume Sequence Annotation And Genbank Submission
Popular Question 6 months ago, created a question with more than 1,000 views. For Automate High-Volume Sequence Annotation And Genbank Submission
Great Question 6 months ago, created a question with more than 5,000 views. For How To Ask Good Questions On Technical And Scientific Forums
Commentator 7 months ago, created a comment with at least 3 up-votes. For C: Biology Introduction For A Computer Scientist
Great Question 8 months ago, created a question with more than 5,000 views. For How To Ask Good Questions On Technical And Scientific Forums
Popular Question 8 months ago, created a question with more than 1,000 views. For Automate High-Volume Sequence Annotation And Genbank Submission
Appreciated 9 months ago, created a post with more than 5 votes. For A: Python 2 Vs Python 3 In Bioinformatics
Appreciated 9 months ago, created a post with more than 5 votes. For A: Python 2 Vs Python 3 In Bioinformatics
Popular Question 10 months ago, created a question with more than 1,000 views. For Automate High-Volume Sequence Annotation And Genbank Submission
Appreciated 13 months ago, created a post with more than 5 votes. For A: Python 2 Vs Python 3 In Bioinformatics
Great Question 13 months ago, created a question with more than 5,000 views. For Code Golf: Mean Length Of Fasta Sequences
Student 13 months ago, asked a question with at least 3 up-votes. For Automate High-Volume Sequence Annotation And Genbank Submission
Popular Question 13 months ago, created a question with more than 1,000 views. For Figure Of Diminishing Sequencing Costs
Popular Question 13 months ago, created a question with more than 1,000 views. For Automate High-Volume Sequence Annotation And Genbank Submission

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