User: maxime.policarpo

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France, Paris
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Posts by maxime.policarpo

<prev • 46 results • page 1 of 5 • next >
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Comment: C: Extract every CDS sequences from a VCF file
... Hi Pierre ! I will try that if I ever need to make this kind of analyses later and I will tell you if it works ! Thanks a lot, Max ...
written 8 weeks ago by maxime.policarpo90
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Answer: A: Extract every CDS sequences from a VCF file
... I found a way to extract the sequences i wanted. For those who wonder how I did : I first extracted the exon strucrure from the gff3 file and placed it on a file called "Gene.structure" I then used bedtools getfasta to extract the corresponding sequence on the Reference genome I then used bcftoo ...
written 9 weeks ago by maxime.policarpo90
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Comment: C: Extract every CDS sequences from a VCF file
... Well this is not very convenient because any indel of the individual mapped to the genome will cause the gff3 to not be phased anymore ...
written 9 weeks ago by maxime.policarpo90
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Comment: C: Extract every CDS sequences from a VCF file
... I would like to make multiple alignments of CDS with the reference sequence and the alternate sequence (For downstream analysis such as dn/ds, analysis of non-syn mutations...) ...
written 9 weeks ago by maxime.policarpo90
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Extract every CDS sequences from a VCF file
... Hi everyone, I have an alignment of genome sequencing reads mapped to a reference genome. I created a VCF file from this alignment and filtered it depending on the PHRED score (>20). Now, I want to extract every CDS sequences that are annotated on the reference genome but with the variants pres ...
vcf cds alignment written 9 weeks ago by maxime.policarpo90 • updated 9 weeks ago by Pierre Lindenbaum124k
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Comment: C: Plot multiple R empricial distributions with different X axis on the same plot
... Hi, Thanks for your answer, but this will create an unique x-axis for all my vectors. I think I will go this way because creating three different X-axis in the same graph dosn't seem very feasible :/ Have a good day, Max ...
written 4 months ago by maxime.policarpo90
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Answer: A: Predict frameshift mutation consequence tool - causing a premature stop codon do
... You can import the WT gene and the gene which contain a frameshift on MEGA and translate prior to alignment to see if it brings a premature stop codon ...
written 4 months ago by maxime.policarpo90
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Plot multiple R empricial distributions with different X axis on the same plot
... Hi, I am facing a problem on which i have to plot three empirical distributions in R with the function "ecdf" but one limitation is that those distributions don't have the same X-axis values. For example I have three vectors : vector1 <- c(-5,-10,-5,-9,-7,-9,-6,-4,-1,-3,-6,-8,-7,-5,-5,-4, ...
R distribution plot written 4 months ago by maxime.policarpo90 • updated 4 months ago by RamRS24k
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Answer: A: What is the difference between blastx and tblastn?
... Blastx will search your sequence in a protein database with a nucleotide sequence as input while tblastn will search in a nucleotide database with a protein input. ...
written 5 months ago by maxime.policarpo90
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Comment: C: Get the divergence between two species with a ref genome and reads
... Thanks for your answer ! I will try to do that :D ...
written 9 months ago by maxime.policarpo90

Latest awards to maxime.policarpo

Teacher 4 months ago, created an answer with at least 3 up-votes. For A: What is the difference between blastx and tblastn?
Popular Question 8 months ago, created a question with more than 1,000 views. For Samtools faidx problem

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