User: jsgounot

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jsgounot130
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4 months ago
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Posts by jsgounot

<prev • 20 results • page 1 of 2 • next >
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Comment: C: Parsing error with Provean : Someone else ?
... Sorry, really old topic and when I look at what I wrote at that time about this, I think I just gave up. ...
written 4 months ago by jsgounot130
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Comment: C: Parse fasta header with regex in python
... Not really important but this should be even better : from Bio import SeqIO infile = "./test.fasta" patterns = ["Eukaryota", "metagenome", "Homo Sapiens", "Mus musculus", "Rattus norvegicus", "Rhizobium", "Gorilla", "beringei", "thaliana", "Oryza sativa", "Dictyos ...
written 20 months ago by jsgounot130
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Comment: C: Scoring whether genes are functional or not based on SIFT and SNPEff results
... Thanks for your answer. Indeed I know that SIFT are only prediction and with no doubt, there are several false positives in the results, however we just want to identify candidate genes in this analysis. Edit : I wrote true positives earlier, sorry for that. ...
written 20 months ago by jsgounot130
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Scoring whether genes are functional or not based on SIFT and SNPEff results
... Hi, I've used SNPEff and SIFT on my dataset (yeast species) and now I have functional annotations of my SNPs and InDels. I would like to score each gene for each sample based on these annotations, with the idea of identifying clusters for which some genes could be functional for some strains and no ...
sift snpeff annotation written 20 months ago by jsgounot130 • updated 20 months ago by Emily_Ensembl18k
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CNV tool for small sequences
... Hi, I've numerous sequences which are not found in the reference genome of my species. I would like to determine the number of copy of these ORFs in each of my individual along with the reference ORFs based on coverage analysis. Most of the softwares I've found use whole genome analysis and don't s ...
tool cnv coverage written 21 months ago by jsgounot130 • updated 21 months ago by bdelolmo10
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Why annotations are not encoded using standard informatic format ?
... Hi, I don't know if this kind of question can be asked on BioStar. I quite don't understand why, with an informatic point of view, current annotations formats as gff, embl, or whatever, are used while standard informatic formats such as json could work. I feel like these formats were used to make ...
open-question encoding annotations written 2.4 years ago by jsgounot130 • updated 2.4 years ago by lh331k
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Obtaining CDS and protein sequences from SNPEff
... Hi, I used SNPEff to determine the impact of SNPs from vcf files and it worked well. However, I would like to obtain the complete coding and protein sequences of the different genes. I know the command dump from SNPEff but I wonder if there is a more easier way to obtain the differents sequences, ...
snpeff written 2.7 years ago by jsgounot130
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Answer: A: Phylogenetic tree based on CNV data
... Thanks for the advises. In the end I have used [SplitsTree][1] with a distance matrix based on euclidean distances (phylip square matrix) and it works well ! [1]: http://www.splitstree.org/ ...
written 2.9 years ago by jsgounot130
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Phylogenetic tree based on CNV data
... Hi, I would like to create an unrooted tree based on CNV data. Such trees were produced in other publication (like the S5 [here][1]) but I don't know which software to use and if I have to transform my data before. What's the best software to do that ? I looked at some but it looks like they only a ...
cnv written 2.9 years ago by jsgounot130
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Comment: C: Mark duplicates fails using samtools view to remove unmapped reads
... Thanks ! It works perfectly now ! ...
written 3.0 years ago by jsgounot130

Latest awards to jsgounot

Popular Question 9 months ago, created a question with more than 1,000 views. For Phylogenetic tree based on CNV data
Popular Question 11 months ago, created a question with more than 1,000 views. For Phylogenetic tree based on CNV data
Popular Question 11 months ago, created a question with more than 1,000 views. For Mark duplicates fails using samtools view to remove unmapped reads
Student 2.4 years ago, asked a question with at least 3 up-votes. For Why annotations are not encoded using standard informatic format ?
Scholar 3.1 years ago, created an answer that has been accepted. For A: Is it possible to check if a sequence has a stop codon, without translating firs
Teacher 3.1 years ago, created an answer with at least 3 up-votes. For A: Is it possible to check if a sequence has a stop codon, without translating firs

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