User: Corentin
Corentin • 450
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PhD student in Bioinformatics, with some experience in RNA-seq and de novo genome assembly.
Posts by Corentin
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... 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 4 months ago by
Corentin • 450
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... 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 5 months ago by
Corentin • 450
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... 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 7 months ago by
Corentin • 450
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... Yes, everything should be linked to the project.
Don't forget WouterDeCouster answer, all of these kmers are not necessarily mis-assemblies. ...
written 8 months ago by
Corentin • 450
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... 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 9 months ago by
Corentin • 450
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... 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 9 months ago by
Corentin • 450
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... 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 9 months ago by
Corentin • 450
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... 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 9 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 10 months ago by
Corentin • 450
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... 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 10 months ago by
Corentin • 450
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