User: Saima

gravatar for Saima
Saima10
Reputation:
10
Status:
New User
Location:
United States
Last seen:
1 year, 9 months ago
Joined:
8 years, 7 months ago
Email:
s*************@gmail.com

Posts by Saima

<prev • 7 results • page 1 of 1 • next >
0
votes
1
answer
1.6k
views
1
answers
Comment: C: How to plot count data by percentile of transcript length for a set of trasncrip
... thanks-- that helped :) ...
written 5.2 years ago by Saima10
1
vote
1
answer
1.6k
views
1
answer
How to plot count data by percentile of transcript length for a set of trasncripts
... 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 ...
R written 5.2 years ago by Saima10 • updated 5.2 years ago by Brice Sarver3.3k
0
votes
1
answer
643
views
1
answers
Comment: C: calculating UTR and CDS feature start and end positions based on transcript leng
... 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 Saima10
0
votes
1
answer
1.7k
views
1
answers
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 ). ...
written 5.3 years ago by Saima10
0
votes
1
answer
9.6k
views
1
answers
Comment: C: Calculate Gene Density Per Kb And Plot Density Over Position For All Scaffolds O
... 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! ...
written 6.7 years ago by Saima10
14
votes
1
answer
9.6k
views
7 follow
1
answer
Calculate Gene Density Per Kb And Plot Density Over Position For All Scaffolds Of A Draft Genome Using R
... 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 ...
gene R written 6.8 years ago by Saima10 • updated 4.7 years ago by archie90
0
votes
3
answers
5.2k
views
3
answers
Comment: C: Calculating Gene Densities From Rnaseq Data
... 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 Saima10

Latest awards to Saima

Popular Question 2.9 years ago, created a question with more than 1,000 views. For How to plot count data by percentile of transcript length for a set of trasncripts
Supporter 5.4 years ago, voted at least 25 times.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1303 users visited in the last hour