User: shalini.ravishankar

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Posts by shalini.ravishankar

<prev • 16 results • page 1 of 2 • next >
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Comment: C: Methylkit using hadoop for DNA analysis
... Can you please explain what do I need to do like steps to achieve this ? It would really help me a lot ...
written 4.6 years ago by shalini.ravishankar10
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Comment: C: Methylkit using hadoop for DNA analysis
... Re implementing in sense ,Do I need to change the whole code ? ...
written 4.6 years ago by shalini.ravishankar10
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Comment: C: Methylkit using hadoop for DNA analysis
... Hi Devon, I was trying to re write but thn I am wondering that my R program takes 3 text files as input and uses a library called methylkit and produces multiple output (mostly PDFs which has charts/graphs) Will this process be affected if I use Hadoop ?? ...
written 4.6 years ago by shalini.ravishankar10
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Comment: C: Methylkit using hadoop for DNA analysis
... thanks devon. I will try it. ...
written 4.6 years ago by shalini.ravishankar10
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Comment: C: Methylkit using hadoop for DNA analysis
... Thanks for information Devon. I will look into the Rhadoop and Rmpi. My concern is, this Methylkit takes input as 3 text files and produces a bunch of files with graphs. Will it create any problem if I use it on Hadoop (RHadoop) ?? ...
written 4.6 years ago by shalini.ravishankar10
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Methylkit using hadoop for DNA analysis
... Hi, Can someone tell me is there a way to do Methylkit ( https://code.google.com/p/methylkit/ ) R Package on Hadoop ??? Please give me some idea on how to proceed this. This is the Code (Original) : library(methylKit) file.list=list( "new_sample1.txt","new_sample2.txt","n_sample3.txt") myobj=re ...
hadoop dna R methylkit written 4.6 years ago by shalini.ravishankar10 • updated 4.6 years ago by RamRS24k
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Hadoop Bam with .bam files
... Hello, I am started learning Hadoop Bam. But couldn't figure out the steps how to to split the bam file.  For example, I have a file called Example.bam. I loaded the file into hdfs :  hadoop fs -put Example.bam ./ When I tried : hadoop jar /usr/local/hadoop-bam/hadoop-bam-7.0.0-jar-with-dep ...
genome hadoop bam hdfs written 4.6 years ago by shalini.ravishankar10 • updated 4.6 years ago by RamRS24k
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Comment: C: Hadoop Streaming for .bam file giving errors
... The use of hadoop is for learning purpose how bio and computer science can co relate with this project.  So you are saying just to load the .bam file to hdfs and run the methratio.py separately on each machine with some scheduler like oozie (in Hadoop ecosystem) ? I am correct ?  If I do so then a ...
written 4.6 years ago by shalini.ravishankar10
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Comment: C: Hadoop Streaming for .bam file giving errors
... Currently we are executing with out hadoop in a single node. But we are trying to use it with hadoop cluster to save processing time and also for learning purpose ...
written 4.6 years ago by shalini.ravishankar10
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Comment: C: Hadoop Streaming for .bam file giving errors
... So it is No way to use with Hadoop in this ?? When you say split the BAM file (2) did you mean load in to hdfs ?? Is there any other way to do this with map reduce ??  ...
written 4.6 years ago by shalini.ravishankar10

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