User: ehzed

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ehzed10
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Posts by ehzed

<prev • 19 results • page 1 of 2 • next >
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What is microbiome community structure?
... I've seen many papers use PCoA plots/beta diversity analysis to describe differences or variation in microbiome structure, usually something along the lines of "the structure was associated with sampling site" or "microbiome structure varied according to treatments". But I am struggling to understan ...
microbiome 16s written 5 days ago by ehzed10 • updated 4 days ago by sacha1.0k
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Confusion regarding generating phylogenetic tree from snp data
... Hi, I am currently comparing multiple breeds of one domestic animal and as part of my analysis, I plan on generating a phylogenetic tree. I started with whole genome sequencing data and since then I have called the snps. Methods I have tried so far (you can skip ahead if you want!): - Tried to ge ...
snps phylogenetic tree written 11 months ago by ehzed10 • updated 11 months ago by Petr Ponomarenko2.4k
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Comment: C: Processing SOLiD data but cannot find relevant documentation on tools (BFAST)
... Thanks for your help! For your dataset, could you tell which reads were forward and which ones were reverse by looking at the headers of each read? Since the paper that I linked didn't give any clear information, I am now trying to figure out what kind of reads I have by looking at the header direct ...
written 14 months ago by ehzed10
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Processing SOLiD data but cannot find relevant documentation on tools (BFAST)
... I realize that almost no one uses SOLiD sequencing anymore, but unfortunately [this paper does][1] and for my project (chicken related) it would be useful to include as many relevant datasets as possible in my analysis. Since a new chicken reference genome assembly came out in January, I need to tak ...
alignment snp sequencing written 14 months ago by ehzed10 • updated 14 months ago by colindaven490
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How do I find raw sequencing data used in publications?
... I know raw sequence data is stored in SRA but the data for this [article][1] isn't found anywhere on there, and the article itself doesn't reference any SRA or BioProject identifier. I know this data must be accessible somewhere because a [later paper][2] used their sequenced reads to perform SNP ca ...
genome next-gen sequencing written 14 months ago by ehzed10
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Comment: C: Value in performing whole genome sequencing on sample size of 1
... Hi Brian, can you elaborate on that? If they only sequence one animal from each breed, they just assume that the snp is found in all animals in that breed, and that the snp didn't arise spontaneously in that one animal? And their only argument for that assumption is that most domestic breeds are inb ...
written 15 months ago by ehzed10
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Value in performing whole genome sequencing on sample size of 1
... All the papers that I've linked below, they performed SNP calling on sequenced reads from one animal for each breed (e.g. sequenced only one Black Angus Bull or one male broiler chicken): [http://www.nature.com/nature/journal/v432/n7018/full/nature03156.html][1] [http://bmcgenomics.biomedcentral.co ...
genome next-gen snp sequencing written 15 months ago by ehzed10 • updated 15 months ago by Brian Bushnell15k
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CNVnator: choosing bin size
... I am trying to select for the best bin size for calling CNVs. In one [post][1], creator of CNVnator said "You can use option ‘-eval’ which will print average RD and standard deviation. We recommend to chose bin size such that the ratio is around 4." I am a little confused about the -eval option beca ...
next-gen cnv written 17 months ago by ehzed10
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Comment: C: Warning from lumpyexpress when calling copy number variants
... Hi trausch, I have paired end data ...
written 18 months ago by ehzed10
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Warning from lumpyexpress when calling copy number variants
... Hello, I am running one of the most basic commands, found on the [lumpy webpage][1]: lumpyexpress -B my.bam -S my.splitters.bam -D my.discordants.bam -o output.vcf to call copy number variants. One of the warnings that I received was "Warning: only 0 elements in distribution (min:1000). I d ...
genome python next-gen lumpy cnv written 18 months ago by ehzed10 • updated 18 months ago by Ram13k

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