User: pradyumna Sagar
pradyumna Sagar • 10
- 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
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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 Sagar • 10
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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 9 days ago by
pradyumna Sagar • 10
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... Did you get the file? please share the link if you get it. ...
written 11 days ago by
pradyumna Sagar • 10
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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 17 days ago by
pradyumna Sagar • 10
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Comment:
C: Primer design shiny app
... link not working anymore ...
written 7 months ago by
pradyumna Sagar • 10
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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 9 months ago by
pradyumna Sagar • 10
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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 11 months ago by
pradyumna Sagar • 10
• updated
11 months ago by
poisonAlien • 2.4k
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... Can you please explain in detail? I am a beginner. ...
written 16 months ago by
pradyumna Sagar • 10
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... 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 Sagar • 10
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... 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 ...
written 17 months ago by
pradyumna Sagar • 10
• updated
1 hour ago by
Phoenix • 100
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