User: Uday Rangaswamy

gravatar for Uday Rangaswamy
Reputation:
100
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Location:
Indian Institute of Technology, Madras, India
Last seen:
8 hours ago
Joined:
1 year ago
Email:
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Posts by Uday Rangaswamy

<prev • 158 results • page 1 of 16 • next >
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Comment: C: Feature extraction from DNA sequence
... I have defined two classes, one contains SNPs taken from an eQTL study involving diseased tissues, and these particular mutations are believed to affect gene expression in context of a particular disease. I've chosen them based on their level of association with the disease in that eQTL study. And, ...
written 8 days ago by Uday Rangaswamy100
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Comment: C: Feature extraction from DNA sequence
... I did go through them. I have a question though. Is it alright to compute conservation score involving the region (eg. 50 bp +/-) surrounding the point of mutation? Because suppose, if positive meant highly conserved and negative meant otherwise, I'd obviously get negative for both my classes. So I ...
written 8 days ago by Uday Rangaswamy100
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Comment: C: Feature extraction from DNA sequence
... I'm sorry I don't think you read my description right. I'm trying to be disease specific in my context. However, I did use ensembl VEP to obtain the positions of rs ids of my interest, in hg38 assembly. Thanks for your thoughts. ...
written 8 days ago by Uday Rangaswamy100
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Comment: C: Feature extraction from DNA sequence
... Both PhyloP and PhastCon score contribute effectively to such classification, and also GC content which gives away about the stability around the variant is also a good predictor along with CpG score. I looked for TSS database in hg38, and I see there is DBTSS but it is not in the format I need. I p ...
written 11 days ago by Uday Rangaswamy100
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Comment: C: Feature extraction from DNA sequence
... Where can I find TSS information? Ensembl? ...
written 15 days ago by Uday Rangaswamy100
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Comment: C: Having issues using UCSC kent tools to convert bigwig file to wig file
... Trying to convert the resulting .wig file to .bed file using : `convert2bed --input=wig [--output=bed] < hg38.phyloP4way.wig > hg38.phyloP4way.bed` Not working though. I get a memory warning while the command runs. Any thoughts? Please help. ...
written 15 days ago by Uday Rangaswamy100
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Comment: C: Having issues using UCSC kent tools to convert bigwig file to wig file
... It solved that particular issue but faced other problems in the later steps. Thanks for your time :). ...
written 17 days ago by Uday Rangaswamy100
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Having issues using UCSC kent tools to convert bigwig file to wig file
... I'm trying to convert a bigwig file to wig file using UCSC kent tools and I'm following the instructions mentioned [here][1]. On entering `mkdir ~/bin/$MACHTYPE` on the command line I get the following error : `mkdir: cannot create directory ‘/home/uday/bin/x86_64-pc-linux-gnu’: No such file or di ...
software error sequence written 17 days ago by Uday Rangaswamy100 • updated 17 days ago by genomax63k
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Comment: C: Feature extraction from DNA sequence
... Got it. Any other feature that would contribute in this context? ...
written 17 days ago by Uday Rangaswamy100
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Comment: C: Feature extraction from DNA sequence
... Yes sir. I'm typing the rest just to fulfill the minimum character criteria. ...
written 18 days ago by Uday Rangaswamy100

Latest awards to Uday Rangaswamy

Voter 17 days ago, voted more than 100 times.
Centurion 3 months ago, created 100 posts.
Supporter 11 months ago, voted at least 25 times.

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