User: pradyumna Sagar
pradyumna Sagar • 20
- Reputation:
- 20
- Status:
- New User
- Location:
- Manipal, School Of Life Sciences
- Website:
- http://pratechsha.com/
- Last seen:
- 3 days, 17 hours ago
- Joined:
- 2 years, 9 months ago
- Email:
- p**************@gmail.com
Posts by pradyumna Sagar
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... I have 10 samples and 1 pooled Control sample will it work good? ...
written 5 months ago by
pradyumna Sagar • 20
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... Hello Everyone,
Can anyone suggest the tool to detection of copy number variation from the data obtained from Ampliseq exome sequencing Iontorrent proton platform. I have tried different tools like Excavator2, cnvkit, FreeC, Ionreporter. Each tool gives different region of CNV from the data. ...
written 5 months ago by
pradyumna Sagar • 20
• updated
5 months ago by
erwan.scaon • 490
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... Excavator2_v1.1.2 provides ucsc.hg19.bw file, I think you can use ucsc's bigWigToWig utility to convert. I am not sure whether it is a good choice. ...
written 5 months ago by
pradyumna Sagar • 20
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Comment:
C: How to run EXCAVATOR2?
... Hi, I just found out that the issue was with the R script in package and the R version I am using. The problem was resolved by changing na.rm value from `na.rm=T` to `na.rm=TRUE` in all the scripts. ...
written 7 months ago by
pradyumna Sagar • 20
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... I have downloaded and installed all the dependencies for excavator2 tool, I have created the target, and while creating data prepare step I ran the following command
`perl EXCAVATORDataPrepare.pl melas_prepare.txt --processors 6 --target melas20k --assembly hg19`
I got the following error:
...
written 7 months ago by
pradyumna Sagar • 20
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... Did you get the file? please share the link if you get it. ...
written 7 months ago by
pradyumna Sagar • 20
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... I have the exact same problem with the sample data, changing the 142 line in conifer.py did not helped. The error is thrown again.
here is the output
Traceback (most recent call last):
File "conifer.py", line 683, in
args.func(args)
File "conifer.py", line 158, in CF_analy ...
written 7 months ago by
pradyumna Sagar • 20
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Comment:
C: Primer design shiny app
... link not working anymore ...
written 15 months ago by
pradyumna Sagar • 20
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... link broken updated link : [http://rna.tbi.univie.ac.at/cgi-bin/RNAWebSuite/RNAfold.cgi][1]
[1]: http://rna.tbi.univie.ac.at/cgi-bin/RNAWebSuite/RNAfold.cgi ...
written 16 months ago by
pradyumna Sagar • 20
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... Hi all,
I found an article on nature (http://www.nature.com/ng/journal/v45/n5/full/ng.2591.html)
where Lego plots were shown which represents mutation frequencies of the samples. How do I replicate the similar kind of graph with the data I have?
I found that MutSigCV can be used to plot the simil ...
written 18 months ago by
pradyumna Sagar • 20
• updated
18 months ago by
poisonAlien • 2.5k
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