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User: Corentin

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Corentin • 430
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PhD student in Bioinformatics, with some experience in RNA-seq and de novo genome assembly.

Posts by Corentin

<prev • 67 results • page 1 of 7 • next >
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Answer: A: Remove character from Fasta IDs -- python
... You are almost there, instead of printing the results to the screen with "print()" you need to use the filehandler you created: "corrected" to **write** to the file. For this you can use the "write()" method, as described in the python documentation (https://docs.python.org/3/tutorial/inputoutput.h ...
written 8 days ago by Corentin • 430
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Comment: C: Assembly and read comparison using kmers
... Yes, everything should be linked to the project. Don't forget WouterDeCouster answer, all of these kmers are not necessarily mis-assemblies. ...
written 4 weeks ago by Corentin • 430
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Comment: C: Assembly and read comparison using kmers
... Not necessarily, depending on the genome size, complexity and the project's budget, there can be more than one library used for the assembly (sometimes from different technologies as well, for example Illumina + PacBio). You should have a Bioproject ID associated with your reads and assembly ("PRJE ...
written 7 weeks ago by Corentin • 430
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Answer: A: Assembly and read comparison using kmers
... In addition to what WouterDeCoster mentioned, it is also possible that these kmers correspond to misassemblies. In general I try to reduce the numbers of kmers found in the assembly and not in the reads as low as possible. Are you using different sets of reads for your assembly ? If yes, these kmer ...
written 7 weeks ago by Corentin • 430
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Answer: A: List of conditions a set of genes are associated with in OMIM
... If you are willing to use R and biomaRt: gene_mart <- biomaRt::useEnsembl(biomart = "ENSEMBL_MART_ENSEMBL", host = "www.ensembl.org", dataset = "hsapiens_gene_ensembl") biomaRt::getBM(mart = gene_mart, ...
written 8 weeks ago by Corentin • 430
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Answer: A: What does gene coordinates "CHR_MG117_PATCH:108783796-108806337"mean?
... I am assuming you are working on the human genome. The human reference genome is still a work in progress, so some areas need improvements, or you can have alternative sequences of the same part of the genome. Instead of waiting for the next release of the human reference, the Genome Reference Con ...
written 8 weeks ago by Corentin • 430
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Comment: C: run_BUSCO.py running problem
... Do you have writing permission for the augustus path you added in the config.ini file? you can check it by running `ls -l ` It will give you the permission for the "owner, group and all", you should check if you are not the owner of the path, you should check if the second before last character i ...
written 3 months ago by Corentin • 430
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Answer: A: Does it make any sense to make a kmer analysis in assembled sequences?
... This does not really make sense, kmer analysis is more useful when applied to reads: The assemblies are often representing only one haplotype, so you will not be able to guess the ploidy from the assembly. Do not forget that the x-axis on the kmer plot represent the frequency of the kmer (how many ...
written 3 months ago by Corentin • 430
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Forum: Plotting Ensembl gene name changes between versions
... I am currently working on ensembl data, and I read about the stable gene identifiers, https://www.ensembl.org/info/genome/stable_ids/index.html Apparently, gene IDs are stable between releases but not necessarily gene names. I got curious and wanted to know if a lot of gene name changes occurred b ...
ensembl forum version R written 3 months ago by Corentin • 430
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Comment: C: SPAdes error during assembly, error code -6
... Are you sure you have access to enough memory on your machine / server ? ...
written 3 months ago by Corentin • 430

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Scholar 8 weeks ago, created an answer that has been accepted. For A: expression to networking
Teacher 8 weeks ago, created an answer with at least 3 up-votes. For A: expression to networking
Popular Question 9 weeks ago, created a question with more than 1,000 views. For RSEM: identical expression for different cufflinks transcripts
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Scholar 9 months ago, created an answer that has been accepted. For A: expression to networking
Appreciated 2.0 years ago, created a post with more than 5 votes. For A: Selecting fastq sequences
Scholar 2.0 years ago, created an answer that has been accepted. For A: expression to networking
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