User: Picasa

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Picasa340
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Posts by Picasa

<prev • 230 results • page 1 of 23 • next >
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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 6 weeks ago by Picasa340 • updated 6 weeks ago by leeandroid50
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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 6 weeks ago by Picasa340
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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 6 weeks ago by Picasa340
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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 7 weeks ago by Picasa340 • updated 7 weeks ago by WouterDeCoster27k
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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 7 weeks ago by Picasa340
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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 10 weeks ago by Picasa340
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Comment: C: Hybrid assembly PacBio Illumina in 2018 ?
... Thanks for your answer jean. PacBio data: Sequel and coverage 20X Illumina data: Total coverage 50X and Insert size: 350, 550, 700 for PE and 3000, 5000 for MP. ...
written 10 weeks ago by Picasa340
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Hybrid assembly PacBio Illumina in 2018 ?
... Hi, Do you have any recommendation for a hybrid assembly of a 1.5G diploid genome using Illumina and Pacbio reads ? I have different insert size libraries with Illumina (paired end and mate pair). I ve seen this page https://github.com/PacificBiosciences/Bioinformatics-Training/wiki/Large-Genom ...
illumina pacbio hybrid assembly written 10 weeks ago by Picasa340 • updated 10 weeks ago by jon.brate150
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Doubt about batch effect and gene expression analysis
... Hello, I am looking for classical gene expression analysis between 2 conditions with the package `limma`. The problem is that the samples have not been sequenced at the same time so I want to introduce a batch effect. This is my model: design <- model.matrix(~Batch + Condition, data = sam ...
gene expression limma batch written 3 months ago by Picasa340 • updated 3 months ago by Kevin Blighe17k
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Comment: C: Average intron length in Drosophila melagnoster
... Thanks for the code, do you know how to get these statistics but per transcript ? so average intron length per transcript for instance ? ...
written 5 months ago by Picasa340

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