User: Aishwarya Kulkarni

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Posts by Aishwarya Kulkarni

<prev • 36 results • page 1 of 4 • next >
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Comment: C: Bulk Download all CDS and UTRs of known genes from ENSEMBL
... Yes I just realized that after posting and perusing through the gtf, just want to confirm.Thanks ...
written 7 weeks ago by Aishwarya Kulkarni60
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Bulk Download all CDS and UTRs of known genes from ENSEMBL
... I want to download all the CDS and UTR coordinates (based on gene id ) from ensembl, is there a way to do that through biomart or biomaRt package? ...
cds utr ensembl written 7 weeks ago by Aishwarya Kulkarni60 • updated 7 weeks ago by ATpoint19k
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How to have frequency displayed on the Y axis in weblogo
... I am using weblogo http://weblogo.berkeley.edu/logo.cgi to try and generate weblogos with frequency (upto 100) displayed on Y axis, I assumed checking the box for frequency plot would do it but I get no display on the Y axis How can it be changed to display frequency on Y axis ? ...
weblogo written 16 months ago by Aishwarya Kulkarni60 • updated 15 months ago by Alex Reynolds28k
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Comment: C: ViennaPackage define output file name and location(RNAplfold)
... Hi @Martombo I am trying to make sense of the results from the -o option and the file looks something like this 1 32 0.0364564 2 30 0.0896707 2 37 0.0202369 2 41 0.135411 3 11 0.0100824 3 29 0.0610271 3 36 0.0134329 3 40 0.0894272 3 54 0.0288916 4 10 0.0104427 4 28 0.0460893 4 ...
written 2.8 years ago by Aishwarya Kulkarni60
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Answer: A: Find transcription factors that bind to inputted nucleotide sequence?
... HOMER is the best tool I have used so far in terms of ease and good documentation , let me know if you need any help with it : http://homer.salk.edu/homer/index.html ...
written 2.8 years ago by Aishwarya Kulkarni60
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Wrapper for RNAplfold
... I am trying to use RNAplfold for target site accessibility of RNA Binding Proteins, has anyone used a good wrapper to use the tool to extract the TAS probability at that binding site. Also what would be the optimum parameters to extract TAS for say for eg a 10 mer binding site? ...
rnaplfold rna-seq bindingsites written 2.8 years ago by Aishwarya Kulkarni60
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Comment: C: Interpretation of RNAplfold
... So does that mean that for the probability of the first 11 mer being unpaired would be under 11 th row and 11 the column i.e at 11-11+1...11? for instance 11 0.6214644 0.5804635 0.5794147 0.5787987 0.5336643 0.512956 0.4683483 0.4437102 0.4185386 0.381642 **0.3854975** The last one will be the ...
written 2.9 years ago by Aishwarya Kulkarni60
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Interpretation of RNAplfold
... Hi I ran RNAplfold as RNAplfold -W 60 -u 11 < trial.fa on a sequence of length 71, it gives me an output of matrix(in the file with extension '_lunp'), with 71 rows and 11 columns, however I didn't quiet get the concept.According to the documentation it says that it will calculate the average p ...
viennapackage rnaplfold rnasecondarystructure written 2.9 years ago by Aishwarya Kulkarni60 • updated 2.9 years ago by Asaf6.1k
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Comment: C: Translating Genomic Locations Between Species
... Based on the blastz scores, how do you determine the conserved sequences, i.e what would be the conservation cutoff? ...
written 3.8 years ago by Aishwarya Kulkarni60
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Comment: C: Using phastCons30way in UCSC table browser
... Hi I checked and 30 way phastcon is the track used to be compared against mouse genome. ...
written 3.8 years ago by Aishwarya Kulkarni60

Latest awards to Aishwarya Kulkarni

Popular Question 3 months ago, created a question with more than 1,000 views. For Conservation score for selected species
Popular Question 3 months ago, created a question with more than 1,000 views. For RNA binding motif
Popular Question 5 months ago, created a question with more than 1,000 views. For Conservation score for selected species
Popular Question 16 months ago, created a question with more than 1,000 views. For Conservation score for selected species
Popular Question 16 months ago, created a question with more than 1,000 views. For Retrieving RNA sequence from corresponding genomic coordinates
Popular Question 16 months ago, created a question with more than 1,000 views. For Tool to calculate extreme most positions in a bed file for a given window
Popular Question 16 months ago, created a question with more than 1,000 views. For Average PhastCon score for a bed file
Popular Question 16 months ago, created a question with more than 1,000 views. For Conservation score for selected species
Popular Question 23 months ago, created a question with more than 1,000 views. For Conservation score for selected species
Popular Question 23 months ago, created a question with more than 1,000 views. For Average PhastCon score for a bed file
Popular Question 2.5 years ago, created a question with more than 1,000 views. For RNA binding motif
Popular Question 2.5 years ago, created a question with more than 1,000 views. For Average PhastCon score for a bed file
Supporter 2.6 years ago, voted at least 25 times.
Popular Question 3.3 years ago, created a question with more than 1,000 views. For Average PhastCon score for a bed file

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