User: guillaume.rbt

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guillaume.rbt370
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France
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27 minutes ago
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Posts by guillaume.rbt

<prev • 104 results • page 1 of 11 • next >
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Comment: C: using two read counting methods with RNA-seq
... Does those tools handle multi-mapping reads? Which may be the best for this task? ...
written 18 hours ago by guillaume.rbt370
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Comment: C: using two read counting methods with RNA-seq
... Thank for the tip, I had a bad feeling about this idea. ...
written 18 hours ago by guillaume.rbt370
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multi-mapped reads counting methods with RNA-seq
... Hi all, I'm currently doing RNA-seq data analysis to assess differential expression between genes. If I understand well, standard methods for counting reads does not take into account reads mapped to multiple loci, which doesn't allow to evaluate expression of duplicated genes. I saw that there i ...
gene count expression rna-seq written 19 hours ago by guillaume.rbt370
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Comment: C: Difference between lower and upper case N in soft masked genome
... thanks :) I missed that one ...
written 8 days ago by guillaume.rbt370
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Comment: C: Can IGV visualize clustal format alignment?
... IGV is not meant to be used to visualize multiple alignment files, maybe you could use the web interface of MAFFT to do your alignement, it will produce a visual output. ...
written 8 days ago by guillaume.rbt370
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Difference between lower and upper case N in soft masked genome
... Hi all, This is maybe a trivial question, but I can't find the answer anywere. I'm working with the soft masked reference genome of Vitis vinifera : ftp://ftp.ensemblgenomes.org/pub/plants/release-38/fasta/vitis_vinifera/dna/Vitis_vinifera.IGGP_12x.dna_sm.toplevel.fa.gz In this file I can find " ...
genome masking reference written 8 days ago by guillaume.rbt370
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Comment: C: Whole genome sequence isolates
... First you have to control the quality of your sequences with fastQC, do a trimming step if needed (trimmomatic,cutadapt), map your sequences to the reference genome (bwa, bowtie2), then you can look for variants, SNPs and/or indels with tools as GATK haplotype caller or Freebayes. I don't know much ...
written 13 days ago by guillaume.rbt370
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Comment: C: Whole genome sequence isolates
... First you have to control the quality of your sequences with fastQC, do a trimming step if needed (trimmomatic,cutadapt), map your sequences to the reference genome (bwa, bowtie2), then you can look for variants, SNPs and/or indels with tools as GATK haplotype caller or Freebayes. I don't know much ...
written 13 days ago by guillaume.rbt370
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Comment: C: Whole genome sequence isolates
... what kind of analysis do you wish to do? ...
written 13 days ago by guillaume.rbt370
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Answer: A: Plotting common SNPs from four individual from a vcf file
... I dont't know a tool that does that directly. But you can extract the SNPs that intersects between your individuals manually and then do Venn diagrams. You can do that with SNPSift for example. see : https://www.biostars.org/p/118384/ ...
written 9 weeks ago by guillaume.rbt370

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Centurion 8 days ago, created 100 posts.
Popular Question 6 weeks ago, created a question with more than 1,000 views. For download protein sequences from NCBI
Great Question 5 months ago, created a question with more than 5,000 views. For Filter genotype in multi-sample VCF file
Popular Question 5 months ago, created a question with more than 1,000 views. For download protein sequences from NCBI
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Scholar 10 months ago, created an answer that has been accepted. For A: Allele count for SNPs
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Scholar 21 months ago, created an answer that has been accepted. For A: Allele count for SNPs
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