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User: Corentin

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Corentin • 450
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PhD student in Bioinformatics, with some experience in RNA-seq and de novo genome assembly.

Posts by Corentin

<prev • 70 results • page 1 of 7 • next >
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Answer: A: manhattan plot for different colorw
... Hi Mag, If you look at the "manhattan" function help, you can see that there is a "col" parameter. (https://rdrr.io/cran/qqman/man/manhattan.html) > col: A character vector indicating which colors to alternate. So you can try to add this parameter to your function call with the color (or color ...
written 12 weeks ago by Corentin • 450
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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 11 months ago by Corentin • 450
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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 12 months ago by Corentin • 450
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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 14 months ago by Corentin • 450
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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 15 months ago by Corentin • 450
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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 16 months ago by Corentin • 450
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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 16 months ago by Corentin • 450
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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 16 months ago by Corentin • 450
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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 16 months ago by Corentin • 450
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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 17 months ago by Corentin • 450

Latest awards to Corentin

Popular Question 5 months ago, created a question with more than 1,000 views. For Timeout on getBM() to retrieve snps from locations
Scholar 12 months ago, created an answer that has been accepted. For A: expression to networking
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Popular Question 16 months ago, created a question with more than 1,000 views. For RSEM: identical expression for different cufflinks transcripts
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Scholar 23 months ago, created an answer that has been accepted. For A: expression to networking
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Scholar 3.2 years ago, created an answer that has been accepted. For A: expression to networking
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