User: Saima
Saima • 10
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- 1 year, 9 months ago
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- 8 years, 7 months ago
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Posts by Saima
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... thanks-- that helped :)
...
written 5.2 years ago by
Saima • 10
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... I have a list of miRNA slicing sites (1 bp-long) for a number of transcripts, and I would like to plot the total count of sites along percentile bins (25th,50th,75th ,100th) of each transcript length for all transcripts. Can anyone please suggest how to do this in R?
My input data looks like this ...
written 5.2 years ago by
Saima • 10
• updated
5.2 years ago by
Brice Sarver • 3.3k
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... I have a different file with transcript ID and site positions (relative to the transcript). The original GFF files have feature positions only as genomic coordinates, but I want to add additional columns for feature positions relative to transcript length to the original reference. I was thinking o ...
written 5.2 years ago by
Saima • 10
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Answer:
A: Plant miRNA prediction
... By clustering miRNAs, do you mean assigning these to a specific miRNA family based on sequence identity? In case of plants, usually mature miRNAs are assigned to the same family based on perfect or near-perfect sequence matches (allowing 0-4 mismatches according to Meyers et al., 2008 paper ).
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written 5.3 years ago by
Saima • 10
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... Thanks a lot for the ggplot solution, it is much better and easier than what I was attempting, and its great that I can extract the plotted data!
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written 6.7 years ago by
Saima • 10
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7 follow
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... I am trying to calculate gene density per 1kb for all scaffolds of a draft genome with IRanges package in R. Based on related posts in biostar and other forums, I have come up with this so far:
test_scaffolds.bed :
scaffold_1 0 2500
scaffold_2 0 6001
test_genes.bed:
scaffold_1 5 ...
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... Hello, I tried to follow your suggestion for calculating gene density but I could not figure out how the successiveIRanges can be used for creating bins for all chromosomes, can you please elaborate your example?
...
written 6.8 years ago by
Saima • 10
Latest awards to Saima
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2.9 years ago,
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For How to plot count data by percentile of transcript length for a set of trasncripts
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3.6 years ago,
created a question with more than 5,000 views.
For Calculate Gene Density Per Kb And Plot Density Over Position For All Scaffolds Of A Draft Genome Using R
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Popular Question
6.8 years ago,
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For Calculate Gene Density Per Kb And Plot Density Over Position For All Scaffolds Of A Draft Genome Using R
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