User: Uday Rangaswamy
Uday Rangaswamy • 120
- Reputation:
- 120
- Status:
- Trusted
- Location:
- Indian Institute of Technology, Madras, India
- Last seen:
- 2 weeks, 2 days ago
- Joined:
- 1 year, 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 16 days ago by
Uday Rangaswamy • 120
4
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191
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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 3 months ago by
Uday Rangaswamy • 120
• updated
9 weeks ago by
Biostar ♦♦ 20
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895
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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 5 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 5 months ago by
Uday Rangaswamy • 120
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895
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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 5 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 5 months ago by
Uday Rangaswamy • 120
0
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895
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... Where can I find TSS information? Ensembl? ...
written 5 months ago by
Uday Rangaswamy • 120
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253
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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 5 months ago by
Uday Rangaswamy • 120
0
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253
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... It solved that particular issue but faced other problems in the later steps. Thanks for your time :). ...
written 5 months ago by
Uday Rangaswamy • 120
4
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1
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253
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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 5 months ago by
Uday Rangaswamy • 120
• updated
5 months ago by
genomax ♦ 70k
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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