User: Uday Rangaswamy
Uday Rangaswamy • 100
- Reputation:
- 100
- Status:
- Trusted
- Location:
- Indian Institute of Technology, Madras, India
- Last seen:
- 8 hours ago
- Joined:
- 1 year ago
- Email:
- m*******@gmail.com
Posts by Uday Rangaswamy
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... 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 Rangaswamy • 100
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... 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 Rangaswamy • 100
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... 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 Rangaswamy • 100
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... 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 Rangaswamy • 100
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... Where can I find TSS information? Ensembl? ...
written 15 days ago by
Uday Rangaswamy • 100
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... 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 Rangaswamy • 100
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... It solved that particular issue but faced other problems in the later steps. Thanks for your time :). ...
written 17 days ago by
Uday Rangaswamy • 100
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... 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 ...
written 17 days ago by
Uday Rangaswamy • 100
• updated
17 days ago by
genomax ♦ 63k
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... Got it. Any other feature that would contribute in this context? ...
written 17 days ago by
Uday Rangaswamy • 100
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... Yes sir. I'm typing the rest just to fulfill the minimum character criteria. ...
written 18 days ago by
Uday Rangaswamy • 100
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