User: Corentin

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Corentin450
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PhD student in Bioinformatics, with some experience in RNA-seq and de novo genome assembly.

Posts by Corentin

<prev • 69 results • page 1 of 7 • next >
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Comment: C: Ambiguous fields in FANTOM 5 Enhancer_TSS_association.bed file
... I did some testing on the UCSC genome browser and it seems that the first three columns correspond to the whole feature (the enhancer + TSS). It is probably to make the genome browser display everything. The coordinates does not exactly match the features (it seems to start before and end after th ...
written 8 months ago by Corentin450
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Answer: A: Ambiguous fields in FANTOM 5 Enhancer_TSS_association.bed file
... Hi, The file is in the BED12 format: http://genome.ucsc.edu/FAQ/FAQformat.html#format1 . This format is used to display tracks on a Genome Browser. The last two columns represents where blocks are drawn on the Genome Browser. **In my understanding**, one block represents the enhancer and the other ...
written 9 months ago by Corentin450
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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 11 months ago by Corentin450
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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 12 months ago by Corentin450
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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 13 months ago by Corentin450
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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 13 months ago by Corentin450
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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 13 months ago by Corentin450
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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 13 months ago by Corentin450
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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 14 months ago by Corentin450
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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 14 months ago by Corentin450

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Popular Question 10 weeks ago, created a question with more than 1,000 views. For Timeout on getBM() to retrieve snps from locations
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