User: guillaume.rbt

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guillaume.rbt340
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340
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Location:
France
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3 weeks, 1 day ago
Joined:
3 years ago
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Posts by guillaume.rbt

<prev • 94 results • page 1 of 10 • next >
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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 7 weeks ago by guillaume.rbt340
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Comment: C: long reads Pacbio SNP calling
... Ok that was what I thought, thanks for your help. ...
written 10 weeks ago by guillaume.rbt340
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Comment: C: Recommended book and courses to study Bioinformatics
... https://www.biostarhandbook.com/ ...
written 10 weeks ago by guillaume.rbt340
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Comment: C: long reads Pacbio SNP calling
... ok great, which tools would you recommend to do that? ...
written 10 weeks ago by guillaume.rbt340
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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 10 weeks ago by guillaume.rbt340 • updated 10 weeks ago by stolarek.ir530
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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 11 weeks ago by guillaume.rbt340
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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 11 weeks ago by guillaume.rbt340
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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 11 weeks ago by guillaume.rbt340
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Comment: C: Merge CNVnator output of multiple samples
... You're welcome ;) ...
written 11 weeks ago by guillaume.rbt340
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Comment: C: Merge CNVnator output of multiple samples
... Yes it's better to merge after, this is the pipeline I use (from the documentation on the github) 1. delly call on each bam : delly call -t DEL -g your_genome.fa -o first_calling_1.bcf your_bam_1.bam delly call -t DEL -g your_genome.fa -o first_calling_2.bcf your_bam_2.bam 2. merge ...
written 11 weeks ago by guillaume.rbt340

Latest awards to guillaume.rbt

Voter 10 weeks ago, voted more than 100 times.
Scholar 5 months ago, created an answer that has been accepted. For A: Allele count for SNPs
Scholar 7 months ago, created an answer that has been accepted. For A: Allele count for SNPs
Teacher 7 months ago, created an answer with at least 3 up-votes. For A: Allele count for SNPs
Commentator 7 months ago, created a comment with at least 3 up-votes. For C: Convert blastn to gff3
Popular Question 14 months ago, created a question with more than 1,000 views. For Filter genotype in multi-sample VCF file
Supporter 15 months ago, voted at least 25 times.
Scholar 15 months ago, created an answer that has been accepted. For A: Allele count for SNPs
Teacher 15 months ago, created an answer with at least 3 up-votes. For A: Allele count for SNPs
Popular Question 20 months ago, created a question with more than 1,000 views. For Filter genotype in multi-sample VCF file
Popular Question 2.2 years ago, created a question with more than 1,000 views. For Filter genotype in multi-sample VCF file

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