User: Picasa
Picasa • 340
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Posts by Picasa
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... 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 ...
written 6 weeks ago by
Picasa • 340
• updated
6 weeks ago by
leeandroid • 50
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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
Picasa • 340
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... 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 ...
written 6 weeks ago by
Picasa • 340
8
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1
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287
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6 follow
1
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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 ...
written 7 weeks ago by
Picasa • 340
• updated
7 weeks ago by
WouterDeCoster ♦ 27k
0
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2
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3.5k
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2
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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
Picasa • 340
0
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1
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415
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1
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... SPAdes is not really designed for medium, big genome ( > 500Mbp) from what I know. ...
written 10 weeks ago by
Picasa • 340
0
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1
answer
415
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1
answers
... 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
Picasa • 340
0
votes
1
answer
415
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1
answer
... 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 ...
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... 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 ...
written 3 months ago by
Picasa • 340
• updated
3 months ago by
Kevin Blighe ♦ 17k
0
votes
5
answers
600
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5
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... 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
Picasa • 340
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