User: akang
akang • 90
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Posts by akang
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... I am trying to run a specific query against specific custom database in python. When i just use one database it works fine but doesnt produce any result (just empty output file) when run my queries against multiple databases. Any suggestions?
db1=os.path.join(path, "ref/db1.fasta")
db2=os.p ...
written 5 weeks ago by
akang • 90
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... I need a suggestion regarding extracting positions from a nucleotide fasta file.
I have a fasta file like below. I am aligning the file ,then converting the sequences into amino acid sequence and finally extracting specific amino acids (say position 1,3,4) from the amino acid data. But since their ...
written 6 weeks ago by
akang • 90
• updated
6 weeks ago by
rpolicastro ♦ 3.9k
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Comment:
C: R, plot text table
... Since it is a biological dataset I think Biostars community suits it the best. This particular problem aims at visualizing a viral gene segment from different samples and understand its origin.
There are all sort of biological datasets and this might be a new one for the community. Here is an examp ...
written 20 months ago by
akang • 90
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Comment:
C: R, plot text table
... Added some information about the example data. ...
written 20 months ago by
akang • 90
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... I have used an R package called Adegenet to calculate pairwise Fst and pairwise genetic distances from an alignment file. But both the values are completely different.
matFst <- pairwise.fst(mydata,res.type="matrix") #pairwise Fst
temp <- pairDistPlot(mydata, other(mydata)$pop) # pai ...
written 2.3 years ago by
akang • 90
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... I have calculated the pairwise distances between populations using adegenet (R package) and have plotted them using a boxplot. Labels on the Y axis are overlapping so i want to change the font size. How do I do that? Here is my code
temp <- pairDistPlot(mydata, grp=mydata$pop)
temp$boxpl ...
written 2.3 years ago by
akang • 90
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... I have 5 groups in my study and I found that within and between mean group genetic distance is greater than 1 when calculated with MEGA X. Can someone help me understand what does that mean?
...
written 2.3 years ago by
akang • 90
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790
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... Is there a program that can calculate effective population size (Ne) based on haploid sequence data? Most programs work with diploid SNP data as I know. ...
written 2.4 years ago by
akang • 90
• updated
6 weeks ago by
chenyangkang24 • 0
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... You can use kinship matrix or GRM which accounts for population structure. For LDAK see –calc-kins-direct and for GCTA see --grm. ...
written 3.5 years ago by
akang • 90
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... I'm trying to do the same thing..just that my data is multi allelic. How do we calculate imputation accuracy for multi allelic data? Ill appreciate any help on that.Thanks! ...
written 3.7 years ago by
akang • 90
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