User: guillaume.rbt

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guillaume.rbt290
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France
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Posts by guillaume.rbt

<prev • 78 results • page 1 of 8 • next >
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Comment: C: Scaffolding with pacbio reads
... Thank you for the publication, I will test some of these tools :) ...
written 4 days ago by guillaume.rbt290
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Comment: C: Scaffolding with pacbio reads
... Hi Shwethacm, Thank you very much for your thorough answer. I understand it is more difficult than I thought to get scaffolds. Actually I've just found out that I have a PE library for some strains (I work on an haploid fungi with a small genome, around 40Mb) How do you think I should use those d ...
written 9 days ago by guillaume.rbt290
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Scaffolding with pacbio reads
... Hi, Sorry for this naive question but I'm a beginner in genome assembly. I'm currently doing Pacbio reads assembly thanks to HGAP, and in result I get a set of contigs. I was wondering if I could, and how, get scaffolds from those contigs. Is it achievable without paired-end reads? Thanks ...
assembly contig scaffold pacbio written 10 days ago by guillaume.rbt290 • updated 8 days ago by shwethacm120
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Answer: A: Coverage analysis of NGS data by Depth
... Hi, You can use bedtools to get the coverage at each base of your alignment : bedtools genomecov -d -ibam your_bam.bam -g your_genome.fa > genome_cov.txt Then you can use a stat tool, as R, to know the percentage of positions above or below a given depth. ...
written 22 days ago by guillaume.rbt290
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Comment: C: Filter SNPs on depth
... I don't know why it doesn't work well, but maybe you could try another tool to filter on depth (ex : snpSift http://snpeff.sourceforge.net/SnpSift.html ) ...
written 24 days ago by guillaume.rbt290
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Comment: C: Extract parts of reads from BAM file that overlap a specific region of genome
... why do you want only a part of the reads? ...
written 26 days ago by guillaume.rbt290
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Comment: C: Splitting the overall RNA-seq data
... With reads you would have to map them against your reference genome to get alignment (bam) files, and then count your reads and perform differential expression between the conditions you're interested in. But it would be easier for you to ask your provider directly for normalized read count, then pe ...
written 5 weeks ago by guillaume.rbt290
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Comment: C: Splitting the overall RNA-seq data
... What kind of files do you have currently? What do you mean by overall analysis? If you have the raw count of each gene in each condition you can maybe redo an analysis to get DEGs between the conditions that you want. ...
written 5 weeks ago by guillaume.rbt290
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Structural variants calling in a population
... Hi all, I'm currently struggling with structural variant calling. I would like to call those structural variants for all samples in my population of haploid fungi (around 100). My aim is to cross the results of all samples to get absence/presence polymorphisms of all called variants. Would anyo ...
structural variants written 5 weeks ago by guillaume.rbt290 • updated 5 weeks ago by Rohit1.2k
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Answer: A: Detect CNVs from SNP data
... Hi, By SNP data do you mean that you have a vcf file? From this kind of data it's difficult to call CNVs. However, if you have the alignments from which the SNPs have been called (bam files) you can run CNV detection tools as pindel, CNVnator or breakdancer ( [https://omictools.com/cnv-detection3 ...
written 6 weeks ago by guillaume.rbt290

Latest awards to guillaume.rbt

Scholar 5 weeks ago, created an answer that has been accepted. For A: Allele count for SNPs
Scholar 3 months ago, created an answer that has been accepted. For A: Allele count for SNPs
Teacher 3 months ago, created an answer with at least 3 up-votes. For A: Allele count for SNPs
Commentator 3 months ago, created a comment with at least 3 up-votes. For C: Convert blastn to gff3
Popular Question 9 months ago, created a question with more than 1,000 views. For Filter genotype in multi-sample VCF file
Supporter 11 months ago, voted at least 25 times.
Scholar 11 months ago, created an answer that has been accepted. For A: Allele count for SNPs
Teacher 11 months ago, created an answer with at least 3 up-votes. For A: Allele count for SNPs
Popular Question 16 months ago, created a question with more than 1,000 views. For Filter genotype in multi-sample VCF file
Popular Question 22 months ago, created a question with more than 1,000 views. For Filter genotype in multi-sample VCF file

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