User: maxime.policarpo

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Posts by maxime.policarpo

<prev • 53 results • page 1 of 6 • next >
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Comment: C: Make tblastn run faster
... Haha yeah this is a lung fish genome that was recently put on the NCBI genome database (Neoceratodus forsteri). I will try to split the genome fasta file into one fasta per scaffold and see if I can get something ... Thanks for the tips and have a good day ! Max ...
written 10 days ago by maxime.policarpo140
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Make tblastn run faster
... Hi everyone and happy new year. I am currently trying to use tblastn using approximately 1000 protein sequences against a genome of 35Gb. However, the time needed is very large even when using multiple threads and it usually does not achieve correctly (Core dumped message) Would anyone have an id ...
genome software tblastn blast written 10 days ago by maxime.policarpo140 • updated 7 days ago by 6schulte20
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Answer: A: Alternative for phylosim in R
... Try this : install_url('http://cran.r-project.org/src/contrib/Archive/compoisson/compoisson_0.3.tar.gz') install_url('http://cran.r-project.org/src/contrib/Archive/phylosim/phylosim_3.0.2.tar.gz') ...
written 7 weeks ago by maxime.policarpo140
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Answer: A: Find overlapping blast hits and keep the highest evalue
... Thanks for your answers ! I finally did it using R and the package GenomicRanges as suggested by Macolm.Cook. I provide the code below : blast_rslt <- read.table("blast_results.tblastn", header=FALSE, sep="\t") colnames(blast_rslt) <- c("query", "sseqid", "pident", "length" ...
written 9 months ago by maxime.policarpo140 • updated 9 months ago by GenoMax95k
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Find overlapping blast hits and keep the highest evalue
... Hi everyone, I am performing tblastn with a set of >1000 proteins as queries against a genome. I am trying to keep every regions of my genome that match a query protein (evalue > 1e-10) but in many cases, 1 genome region will have many hits (several queries in the same region). This is mos ...
genome R blast written 9 months ago by maxime.policarpo140
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Answer: A: tblastn extend beyond homology region
... Are you trying to find the orthologous sequence from your protein in a genome ? If so, you can just extract your tblastn region with samtools faidx (like 100000bp upstream + 100000bp downstream) and then use exonerate to find the CDS of your gene on this genome, which will give you the exon sequence ...
written 11 months ago by maxime.policarpo140
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ABC method - Number of individuals
... Hi, I am about to use DIYABC with SNPs derived from genomic data. I used GATK to make variant calls followed by hard-filters as suggested in their variant discovery pipeline (Only SNP variants were kept). My gVCF file is composed of 5 populations of the same species (pop1 : 9 individuals, pop2: 6 i ...
population genetics abc diyabc written 13 months ago by maxime.policarpo140
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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 16 months ago by maxime.policarpo140
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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 16 months ago by maxime.policarpo140
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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 16 months ago by maxime.policarpo140

Latest awards to maxime.policarpo

Popular Question 10 days ago, created a question with more than 1,000 views. For How to generate a new FASTA from an assembly-assembly mapping ?
Scholar 7 weeks ago, created an answer that has been accepted. For A: Find overlapping blast hits and keep the highest evalue
Popular Question 8 months ago, created a question with more than 1,000 views. For How to generate a new FASTA from an assembly-assembly mapping ?
Scholar 9 months ago, created an answer that has been accepted. For A: Find overlapping blast hits and keep the highest evalue
Popular Question 11 months ago, created a question with more than 1,000 views. For Rna-Seq alignment with genome
Teacher 19 months ago, created an answer with at least 3 up-votes. For A: What is the difference between blastx and tblastn?
Popular Question 23 months ago, created a question with more than 1,000 views. For Samtools faidx problem

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