User: guillaume.rbt

gravatar for guillaume.rbt
guillaume.rbt330
Reputation:
330
Status:
Trusted
Location:
France
Last seen:
4 days, 7 hours ago
Joined:
2 years, 10 months ago
Email:
g************@gmail.com

Posts by guillaume.rbt

<prev • 93 results • page 1 of 10 • next >
0
votes
1
answer
124
views
1
answers
Comment: C: long reads Pacbio SNP calling
... Ok that was what I thought, thanks for your help. ...
written 7 days ago by guillaume.rbt330
2
votes
1
answer
180
views
1
answers
Comment: C: Recommended book and courses to study Bioinformatics
... https://www.biostarhandbook.com/ ...
written 7 days ago by guillaume.rbt330
0
votes
1
answer
124
views
1
answers
Comment: C: long reads Pacbio SNP calling
... ok great, which tools would you recommend to do that? ...
written 7 days ago by guillaume.rbt330
3
votes
1
answer
124
views
1
answer
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 7 days ago by guillaume.rbt330 • updated 7 days ago by stolarek.ir530
0
votes
0
answers
147
views
0
answers
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 13 days ago by guillaume.rbt330
0
votes
0
answers
147
views
0
answers
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 14 days ago by guillaume.rbt330
0
votes
0
answers
147
views
0
answers
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 14 days ago by guillaume.rbt330
0
votes
0
answers
164
views
0
answers
Comment: C: Merge CNVnator output of multiple samples
... You're welcome ;) ...
written 14 days ago by guillaume.rbt330
1
vote
0
answers
164
views
0
answers
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 15 days ago by guillaume.rbt330
0
votes
0
answers
164
views
0
answers
Comment: C: Merge CNVnator output of multiple samples
... I had the same problem and I haven't found any available tool to merge output from CNVnator... I eventually used delly2 to find structural variants, because it handles multi-sample calling. ...
written 29 days ago by guillaume.rbt330

Latest awards to guillaume.rbt

Voter 7 days ago, voted more than 100 times.
Scholar 3 months ago, created an answer that has been accepted. For A: Allele count for SNPs
Scholar 5 months ago, created an answer that has been accepted. For A: Allele count for SNPs
Teacher 5 months ago, created an answer with at least 3 up-votes. For A: Allele count for SNPs
Commentator 5 months ago, created a comment with at least 3 up-votes. For C: Convert blastn to gff3
Popular Question 11 months ago, created a question with more than 1,000 views. For Filter genotype in multi-sample VCF file
Supporter 13 months ago, voted at least 25 times.
Scholar 13 months ago, created an answer that has been accepted. For A: Allele count for SNPs
Teacher 13 months ago, created an answer with at least 3 up-votes. For A: Allele count for SNPs
Popular Question 18 months ago, created a question with more than 1,000 views. For Filter genotype in multi-sample VCF file
Popular Question 24 months ago, created a question with more than 1,000 views. For Filter genotype in multi-sample VCF file

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 770 users visited in the last hour