User: Uday Rangaswamy
Uday Rangaswamy • 120
- Reputation:
- 120
- Status:
- Trusted
- Location:
- Indian Institute of Technology, Madras, India
- Last seen:
- 11 months, 2 weeks ago
- Joined:
- 2 years, 5 months ago
- Email:
- m*******@gmail.com
Posts by Uday Rangaswamy
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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 12 months ago by
Uday Rangaswamy • 120
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... 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. ...
written 15 months ago by
Uday Rangaswamy • 120
• updated
13 months ago by
Biostar ♦♦ 20
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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 17 months ago by
Uday Rangaswamy • 120
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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 17 months ago by
Uday Rangaswamy • 120
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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 17 months ago by
Uday Rangaswamy • 120
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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 17 months ago by
Uday Rangaswamy • 120
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1.5k
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... Where can I find TSS information? Ensembl? ...
written 17 months ago by
Uday Rangaswamy • 120
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1
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511
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1
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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 17 months ago by
Uday Rangaswamy • 120
0
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511
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... It solved that particular issue but faced other problems in the later steps. Thanks for your time :). ...
written 17 months ago by
Uday Rangaswamy • 120
4
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1
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511
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1
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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 months ago by
Uday Rangaswamy • 120
• updated
17 months ago by
genomax ♦ 87k
Latest awards to Uday Rangaswamy
Popular Question
15 months ago,
created a question with more than 1,000 views.
For Differential expression gene analysis
Popular Question
15 months ago,
created a question with more than 1,000 views.
For DESeq2 modelling and Wald's test
Voter
17 months ago,
voted more than 100 times.
Centurion
20 months ago,
created 100 posts.
Supporter
2.3 years ago,
voted at least 25 times.
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