User: Picasa

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Picasa350
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Posts by Picasa

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Inversion detection between 2 genomes
... Hi all, I am comparing two very similar genomes and looking to see whether there are some part that are rearranged such as inversion. Do you know any tools that can help me to do this ? By the past, I used nucmer but if you know something else, I would be happy to hear. Thanks ! ...
genome inversion written 10 days ago by Picasa350 • updated 10 days ago by WouterDeCoster29k
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n50 contig with pacbio nowadays ?
... Hi, I am looking for that kind of picture : https://www.pacb.com/wp-content/uploads/2014/02/fig1-1024x422.png but it's a it outdated. Do you have something similar for 2017-2018 ? Thanks for your help. ...
n50 pacbio written 25 days ago by Picasa350
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Comment: C: Doubt on removing duplicates on amplicon sequencing data
... Thanks Devon, I have edited my post with another question. Maybe you have not seen it: 3) There are 2 type of duplicates: optical and pcr, in that case do I have to remove only optical duplicates ? if yes, do you know how ? seems that Picard doest not separate optical and pcr. ...
written 5 weeks ago by Picasa350
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Doubt on removing duplicates on amplicon sequencing data
... Hi, I am looking to make a simple SNP analysis. I have different individuals from which we have targeted specific markers. Then the reads I have come from amplicon sequencing. My questions are: 1) Do I have to remove duplicates ? From what I understand, tools like Picard look for the same 5', b ...
duplicates amplicon written 5 weeks ago by Picasa350 • updated 5 weeks ago by Devon Ryan81k
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From a vcf SNP file to a phylogenetic tree
... Hi everybody, I have made a vcf file with GATK that include SNPs from 10 samples. My goal is to make a phylogenetic tree of SNPs, Can you redirect me toward a ressource than explain what is the possibilities from a VCF file ?. I have imagined making a fasta file and feed it to phylogenetic infe ...
vcf phylogenetic snp written 3 months ago by Picasa350 • updated 3 months ago by leeandroid80
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Comment: C: GATK combine gvcf superslow
... I am working on a non model organism, with a genome that have been assembled. Unfortunately, this is quite fragmented. Is is still worth do it ? ...
written 3 months ago by Picasa350
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GATK combine gvcf superslow
... Hi, I am working on a classic variant calling on a non model organism. I have 250 samples and followed the GATK best practice. I have produced 250 g.vcf with HaplotypeCaller, now the next step is to combine those g.vcf and produce a .vcf (with GenotypeGVCFs) either: A) Solution A: using Genomics ...
gatk combinegvcfs genomicsdbimport written 3 months ago by Picasa350
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Forum: SNP calling in 2018
... Hi ! I would like to perform a simple variant analysis (SNP) with multi samples. I use to used the GATK workflow before but I would like to know if there is anything "better" than GATK nowaday, or is it always the gold standard ? Thanks ...
gatk forum variant snp written 3 months ago by Picasa350 • updated 3 months ago by WouterDeCoster29k
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Comment: C: About The Priority Of Trimming
... Hi Devon, do you have a source for "There's no need to trim these bases off (eg. the ~10bp at the 5' end) , they won't actually bias mapping". ...
written 3 months ago by Picasa350
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Comment: C: Hybrid assembly PacBio Illumina in 2018 ?
... SPAdes is not really designed for medium, big genome ( > 500Mbp) from what I know. ...
written 4 months ago by Picasa350

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