User: pradyumna Sagar

Reputation:
20
Status:
New User
Location:
Manipal, School Of Life Sciences
Website:
http://pratechsha.com/
Last seen:
1 week, 4 days ago
Joined:
3 years ago
Email:
p**********@learner.manipal.edu

Posts by pradyumna Sagar

<prev • 13 results • page 1 of 2 • next >
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Comment: C: Tools for Copy Number Variation analysis from ion Proton data.
... I have 10 samples and 1 pooled Control sample will it work good? ...
written 8 months ago by pradyumna Sagar20
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Tools for Copy Number Variation analysis from ion Proton data.
... 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. ...
iontorrent-proton ampliseq ngs next-gen cnv written 8 months ago by pradyumna Sagar20 • updated 8 months ago by erwan.scaon550
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Comment: C: Looking for wig base coverage file for hg19
... 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 8 months ago by pradyumna Sagar20
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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 9 months ago by pradyumna Sagar20
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How to run EXCAVATOR2?
... 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: ...
R excavator2 written 10 months ago by pradyumna Sagar20
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Comment: C: Looking for wig base coverage file for hg19
... Did you get the file? please share the link if you get it. ...
written 10 months ago by pradyumna Sagar20
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Comment: C: Error ecountered while running conifer with demo data set
... 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 10 months ago by pradyumna Sagar20
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Comment: C: Primer design shiny app
... link not working anymore ...
written 17 months ago by pradyumna Sagar20
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Comment: C: Programs for RNA secondary structure predictions
... 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 19 months ago by pradyumna Sagar20
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How to draw lego plot Using Mutation Data (MAF format input)?
... 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 ...
genome next-gen mutation sequencing written 21 months ago by pradyumna Sagar20 • updated 21 months ago by poisonAlien2.5k

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