User: cyril-cros

gravatar for cyril-cros
cyril-cros840
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840
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Location:
France
Last seen:
2 years, 5 months ago
Joined:
3 years, 10 months ago
Email:
c*********@hotmail.fr

Posts by cyril-cros

<prev • 150 results • page 1 of 15 • next >
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Comment: C: Personalized Medicine + Bioinformatics
... The National Human Genome Research Institute (US) might be a first place to look up. Its director (Eric D. Green) gave a speech on personalized medicine at my university and is pretty much into it, but I was working in the lab.... ...
written 2.9 years ago by cyril-cros840
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How to identify the ancestral population to which an individual belongs knowing its allele frequencies?
... Hi, I have been given as part as a homework a set of genotyped human SNP for many individuals; I am supposed to identify their ancestral populations (disclaimer: as a bonus question I won't submit and which is likely an example from the readings I have to do, so I am not asking for a key in hand sol ...
infer ancestry structure snp written 2.9 years ago by cyril-cros840 • updated 2.9 years ago by stolarek.ir570
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Comment: C: How can I know what genes each Trinity ID are ?
... Just be careful, Blat shows you similar segments. Orthologous genes may be a problem here... ...
written 3.0 years ago by cyril-cros840
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Answer: A: How can I know what genes each Trinity ID are ?
... Now, for a correct answer. You are doing mice which is a really well annotated organism. Trinity will be imprecise. You would be way better using Cufflinks with the reference genome and annotation, if you are looking for novel  isoforms or things like that it will find them for you. Are trying to a ...
written 3.0 years ago by cyril-cros840
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Comment: C: How can I know what genes each Trinity ID are ?
... Same with mine. Transcripts generated by Trinity are strand-specific. However, you are including reads that may be the product of antisense transcription. EDIT: I made a mistake, trinity outputs a fasta file and not a gtf or bed file... ...
written 3.0 years ago by cyril-cros840
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Answer: A: Difference Between SNP and Single Point Mutation in Cancer
... Just another point about SNPs: they are defined as DNA sequence variations between individuals in a given population, and they have to be found in a significant fraction of your particular population (more than 1% typically).  The key point is that there will be more variants specific to the indivi ...
written 3.0 years ago by cyril-cros840
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Answer: A: How can I know what genes each Trinity ID are ?
... Disclaimer: I forgot Trinity outputs a fasta file and not a GTF or BED. Bad answer, but might be useful to someone I had that same issue with another tool (https://github.com/shenkers/isoscm ). Your best bet is to use bedtools/bedops. My scripts are not really portable (working on it, who knows it ...
written 3.0 years ago by cyril-cros840
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Comment: C: Alignment tool for splicing analysis
... STAR stores a lot of data in RAM. If you have access to good hardware, it is lightning fast. ...
written 3.1 years ago by cyril-cros840
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Answer: A: Can OMA calculate orthologs for single query sequence?
... You have a very large many number of databases with precomputed groups of orthologs. Try http://orthodb.org/ which is quite complete. Another technique is to look at genes in the vicinity of your protein, they may be part of a synteny group. ...
written 3.1 years ago by cyril-cros840
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Comment: C: what is the biological replications
... You can try a first batch of 3-4 replicates just to see if there is something, but you can't easily do legitimate statistics by combining different batches (your experimental conditions change). 6-7 reps would be what is needed for a publication. ...
written 3.1 years ago by cyril-cros840

Latest awards to cyril-cros

Popular Question 2.4 years ago, created a question with more than 1,000 views. For Bedtools: merge all features with the same id
Popular Question 2.8 years ago, created a question with more than 1,000 views. For Bedtools: merge all features with the same id
Popular Question 2.8 years ago, created a question with more than 1,000 views. For How to subset a bed or gtf file to some genes of interest?
Scholar 3.0 years ago, created an answer that has been accepted. For A: Tips to speed up read.fasta() in R for large files?
Supporter 3.1 years ago, voted at least 25 times.
Centurion 3.3 years ago, created 100 posts.
Teacher 3.4 years ago, created an answer with at least 3 up-votes. For A: Can I use own transcriptome without GTF file?
Scholar 3.4 years ago, created an answer that has been accepted. For A: Tips to speed up read.fasta() in R for large files?
Appreciated 3.5 years ago, created a post with more than 5 votes. For C: KeyError: "no key 'chr11' in database " in python
Teacher 3.5 years ago, created an answer with at least 3 up-votes. For A: Can I use own transcriptome without GTF file?
Good Answer 3.5 years ago, created an answer that was upvoted at least 5 times. For C: KeyError: "no key 'chr11' in database " in python
Teacher 3.5 years ago, created an answer with at least 3 up-votes. For A: Can I use own transcriptome without GTF file?
Scholar 3.5 years ago, created an answer that has been accepted. For A: Tips to speed up read.fasta() in R for large files?
Teacher 3.5 years ago, created an answer with at least 3 up-votes. For A: Can I use own transcriptome without GTF file?
Appreciated 3.6 years ago, created a post with more than 5 votes. For C: KeyError: "no key 'chr11' in database " in python
Commentator 3.6 years ago, created a comment with at least 3 up-votes. For C: desktop bioinformatics platform specs
Commentator 3.6 years ago, created a comment with at least 3 up-votes. For C: desktop bioinformatics platform specs
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Scholar 3.6 years ago, created an answer that has been accepted. For A: Tips to speed up read.fasta() in R for large files?
Scholar 3.6 years ago, created an answer that has been accepted. For A: Tips to speed up read.fasta() in R for large files?
Scholar 3.7 years ago, created an answer that has been accepted. For A: Tips to speed up read.fasta() in R for large files?

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