User: micro32uvas

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micro32uvas10
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New User
Location:
Pakistan
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2 weeks, 4 days ago
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4 years ago
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m**********@gmail.com

Posts by micro32uvas

<prev • 61 results • page 1 of 7 • next >
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Venn diagram for ~12 shared SNP data
... Hi, I am working on around 12 breeds from my region. Now I want to present my data, is representing one civilization or a country. I want to represent their sharing and uniqueness. One ways to show the breed specific in a boring bar diagram, where shaded part represents breed specific and other i ...
sharedsnps venn uniquesnps breedspecific written 18 days ago by micro32uvas10 • updated 18 days ago by Asaf6.5k
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Comment: C: PCA cannot separate different breeds
... Thank you Mensur Dlakic, And yes the sum of all the three components is ~9-10%. I am unaware of t-SNE but i will definately look into it. and update her, if I get any difference. ...
written 4 months ago by micro32uvas10
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Comment: C: PCA cannot separate different breeds
... Thank you Jean-Karim Heriche for the guidance. I used three components PC1, PC2, PC3 to plot three kinds of PCA but results were comparatable. As per the paper and your suggestion, if I increase the LD or other parameters for SNP selection, could I still seperate them? Could you explain a bit mor ...
written 4 months ago by micro32uvas10
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Comment: C: PCA cannot separate different breeds
... Thank you very much Carambakaracho for your response. The main question is about the PCA and the clustering related to it. The variant calling is fine, as i have followed the 1000bull genome pipeline and it has worked well so far. The problem starts when the 11 breeds cover an entire country with ...
written 4 months ago by micro32uvas10
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PCA cannot separate different breeds
... Hello everyone, I have WGS data of 118 samples, out of which 72 are from one country, consisting of 11 breeds , that are under consideration. I used others to distinguish/ control. After running the NJ tree from the called SNP data, I ran PCA which separates 72 and 46 (The 46 clearly clusters into ...
wgs pca admix snp tree written 4 months ago by micro32uvas10 • updated 4 months ago by RamRS25k
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Comment: C: Addition of Y chromosome to the ref sequence
... What I dont get, is that the providers of the ref seq, (NCBI and Bovine database) have not given any newer version for the said purpose (The latest came by April 2018, and its done by PacBio). Now one of the pipelines, shared by the 1000 Bull genome Project, includes the Ref Seq (NCBI's Ref seq+ Y) ...
written 8 months ago by micro32uvas10
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Addition of Y chromosome to the ref sequence
... Hello, I have aligned my WGS samples to a the latest bovine reference(B.tau5.0), available at NCBI. It is just yesterday, that in a pipeline used by 1000bull genome project, they have used the same reference merging the Y chromosome in it (B.taur5.0Y). Now, I am not sure about it. Should I align ...
assembly alignment bwa written 8 months ago by micro32uvas10 • updated 8 months ago by Devon Ryan93k
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Beauti and Beast
... Hello, I am working on bayesian analysis. I run BEAUTI and BEAST for MCMC runs for BSP analysis. I need to set 32% nucleotide substitution per million years but i cannot figure it out well. Can anyone help me out in the result interpretation. Ainnie ...
tracer nucleotide substitution per million year written 10 months ago by micro32uvas10 • updated 9 months ago by Biostar ♦♦ 20
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Arlequin interpretation for demography and molecular indices
... Hi there, I used Arlequin for a Molecular indices, demographic expansions, comparing the pairwise distances and pairwise Fst between 5 groups. Now that i got the results, I cannot figure out how to interpret them as well as if my deduced results are right. Can anyone help me in reading the arlequi ...
pairwisefst demographic expansion arlequin written 10 months ago by micro32uvas10
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Comment: C: NovoPlasty is producing identical Assemblies
... Yeah and to combat this issue, I went with Sanger for the confirmation. Turned out there was read depth problem at some locations, in case of multiple assemblies. They didn't vary much but few of them made multiple. Ruled the problem out by Sanger. ...
written 13 months ago by micro32uvas10

Latest awards to micro32uvas

Popular Question 8 months ago, created a question with more than 1,000 views. For Convertion to gff3 format
Popular Question 9 months ago, created a question with more than 1,000 views. For Convertion to gff3 format
Popular Question 12 months ago, created a question with more than 1,000 views. For Viral Encoded miRNA prediction and target identification
Popular Question 12 months ago, created a question with more than 1,000 views. For Bowtie2 alignment error
Popular Question 23 months ago, created a question with more than 1,000 views. For bowtie2-align died with signal 6 (ABRT) (core dumped)

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