User: guillaume.rbt

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guillaume.rbt360
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France
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4 days, 22 hours ago
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3 years, 3 months ago
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Posts by guillaume.rbt

<prev • 95 results • page 1 of 10 • next >
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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 4 days ago by guillaume.rbt360
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Comment: C: CNV calling on tumor sample with no germline counterpart
... I personally use Delly2, which seems to work well (I'm working on haploid fungi) ...
written 4 months ago by guillaume.rbt360
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Comment: C: long reads Pacbio SNP calling
... Ok that was what I thought, thanks for your help. ...
written 5 months ago by guillaume.rbt360
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Comment: C: Recommended book and courses to study Bioinformatics
... https://www.biostarhandbook.com/ ...
written 5 months ago by guillaume.rbt360
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Comment: C: long reads Pacbio SNP calling
... ok great, which tools would you recommend to do that? ...
written 5 months ago by guillaume.rbt360
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long reads Pacbio SNP calling
... Hi all, I understand that with Pacbio error rate (~15%), it is not really suitable for SNP calling. This is maybe a naive question, but I was wondering if we have, for example, a really high coverage sequencing of a bacteria (>200X), wouldn't it make it possible to call SNP anyway? If so, wha ...
pacbio snp written 5 months ago by guillaume.rbt360 • updated 9 weeks ago by tjduncan100
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Comment: C: Searching for the common sequences in multiple (>2) fastq files
... To get the coverage I personally use bedtools : bedtools genomecov -d -ibam your_bam_1.bam -g your_genome.fa > coverage_1.txt & ...
written 5 months ago by guillaume.rbt360
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Comment: C: Searching for the common sequences in multiple (>2) fastq files
... The regions where you will have a minimum coverage on all bams will have matching reads from all the fastq. For example if you take a threshold of 5X, for a given position on the genome, at least 5 reads on each fastq is mapped on this position. As all those reads will be matching the same regions ...
written 5 months ago by guillaume.rbt360
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Comment: C: Searching for the common sequences in multiple (>2) fastq files
... Hi, To do that I would align the reads from all the fastq you have on your reference genome. Then I would detect regions where a minimum coverage is present on all of 15 bams, then extract the reads from those regions. If they align all to the same regions, they should be similar. ...
written 5 months ago by guillaume.rbt360
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Comment: C: Merge CNVnator output of multiple samples
... You're welcome ;) ...
written 5 months ago by guillaume.rbt360

Latest awards to guillaume.rbt

Great Question 3 months ago, created a question with more than 5,000 views. For Filter genotype in multi-sample VCF file
Popular Question 3 months ago, created a question with more than 1,000 views. For download protein sequences from NCBI
Popular Question 3 months ago, created a question with more than 1,000 views. For nb spanning reads confusion in Tophat Fusion output
Voter 5 months ago, voted more than 100 times.
Scholar 8 months ago, created an answer that has been accepted. For A: Allele count for SNPs
Scholar 10 months ago, created an answer that has been accepted. For A: Allele count for SNPs
Teacher 10 months ago, created an answer with at least 3 up-votes. For A: Allele count for SNPs
Commentator 10 months ago, created a comment with at least 3 up-votes. For C: Convert blastn to gff3
Popular Question 17 months ago, created a question with more than 1,000 views. For Filter genotype in multi-sample VCF file
Supporter 18 months ago, voted at least 25 times.
Scholar 18 months ago, created an answer that has been accepted. For A: Allele count for SNPs
Teacher 18 months ago, created an answer with at least 3 up-votes. For A: Allele count for SNPs
Popular Question 23 months ago, created a question with more than 1,000 views. For Filter genotype in multi-sample VCF file
Popular Question 2.4 years ago, created a question with more than 1,000 views. For Filter genotype in multi-sample VCF file

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