User: Uday Rangaswamy

gravatar for Uday Rangaswamy
Reputation:
120
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Trusted
Location:
Indian Institute of Technology, Madras, India
Last seen:
2 weeks, 2 days ago
Joined:
1 year, 5 months ago
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m*******@gmail.com

Posts by Uday Rangaswamy

<prev • 160 results • page 1 of 16 • next >
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Comment: C: Bedtools BEDMAP usage
... foreach ($v1 as $value) { $outputh = system("/home/uday/anaconda3/bin/bedmap --chrom ". $value ." --mean ppCkrtYdyJ_3.bed pc.bed >> ppCkrtYdyJ_f10.txt"); } v1 contains unique chromosomes. I'm getting an empty file as output. ...
written 16 days ago by Uday Rangaswamy120
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bedops bedmap operation in python
... I noticed there is a conda version of bedops bedmap function available. I've been struggling to use it though. Could someone refer me to any documentation of it's usage in a python script please. Have a great day. Thanks in advance. ...
python bedops bedmap written 3 months ago by Uday Rangaswamy120 • updated 9 weeks ago by Biostar ♦♦ 20
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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 5 months ago by Uday Rangaswamy120
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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 5 months ago by Uday Rangaswamy120
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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 5 months ago by Uday Rangaswamy120
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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 5 months ago by Uday Rangaswamy120
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Comment: C: Feature extraction from DNA sequence
... Where can I find TSS information? Ensembl? ...
written 5 months ago by Uday Rangaswamy120
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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 5 months ago by Uday Rangaswamy120
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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 5 months ago by Uday Rangaswamy120
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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 5 months ago by Uday Rangaswamy120 • updated 5 months ago by genomax70k

Latest awards to Uday Rangaswamy

Popular Question 3 months ago, created a question with more than 1,000 views. For Differential expression gene analysis
Popular Question 3 months ago, created a question with more than 1,000 views. For DESeq2 modelling and Wald's test
Voter 5 months ago, voted more than 100 times.
Centurion 8 months ago, created 100 posts.
Supporter 16 months ago, voted at least 25 times.

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