User: pradyumna Sagar

Reputation:
10
Status:
New User
Location:
Manipal, School Of Life Sciences
Website:
http://pratechsha.com/
Last seen:
an hour ago
Joined:
2 years, 2 months ago
Email:
p**************@gmail.com

Posts by pradyumna Sagar

<prev • 10 results • page 1 of 1 • next >
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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 1 hour ago by pradyumna Sagar10
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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 9 days ago by pradyumna Sagar10
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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 11 days ago by pradyumna Sagar10
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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 17 days ago by pradyumna Sagar10
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Comment: C: Primer design shiny app
... link not working anymore ...
written 7 months ago by pradyumna Sagar10
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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 9 months ago by pradyumna Sagar10
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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 11 months ago by pradyumna Sagar10 • updated 11 months ago by poisonAlien2.4k
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Comment: C: How to extract a region from a reference sequence which does not align with a gi
... Can you please explain in detail? I am a beginner. ...
written 16 months ago by pradyumna Sagar10
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Comment: C: How to extract a region from a reference sequence which does not align with a gi
... what if i do not know the coordinate regions? I mean as I have mentioned I have to perform this nearly 200 times so it will be difficult to check the coordinates of the reference file which do not match with my query each time. Can you help me with a solution which will directly extract the unaligne ...
written 16 months ago by pradyumna Sagar10
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How to extract a region from a reference sequence which does not align with a given query read?
... I have a query sequence with 1935 bp and a reference sequence with 2817 bp. My query aligns fully with the reference sequence. I need to extract the regions from the reference sequence(2817bp) which are not a part of my query i.e.approximately 882 bp. I need to do this for many such files (nearly 20 ...
genome sequence next-gen alignment sequencing written 17 months ago by pradyumna Sagar10 • updated 1 hour ago by Phoenix100

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