Question: Genome data on hadoop chromosome level
0
gravatar for shalini.ravishankar
4.2 years ago by
shalini.ravishankar0 wrote:
Hello Everyone, I am an IT student doing some work on hadoop in human genome project. My first trouble is how do I store the genome data in hadoop cluster ? How do I store data Chromosome wise ? We do have cluster of 30 machines with hadoop. The problem is we are planning to process the human genome project using hadoop. Here the data is in the form of BAM files. I know if I load the data to hdfs, it will automatically split it into chunks and store on the name nodes. Thats is the problem here. I couldn't split the data like that. Need to split the data chromosome wise so that we can perform bio algorithm computing on them. Bio algorithm computing : for instance bisulfite methylation extraction. Currently we use bismap ( python tool ). Is there a way to store the data chromosome wise on hadoop.and run the bismap tool command as map reduce jobs
chromosome nga hadoop genome • 1.7k views
ADD COMMENTlink modified 4.2 years ago • written 4.2 years ago by shalini.ravishankar0
2

Hello shalini.ravishankar!

It appears that your post has been cross-posted to another site: SEQanswers.

This is typically not recommended as it runs the risk of annoying people in both communities.

ADD REPLYlink written 4.2 years ago by Devon Ryan88k
Thanks Alex. Sure I will take a look in to that.
ADD REPLYlink written 4.2 years ago by shalini.ravishankar0

cross-posted on SO: http://stackoverflow.com/questions/27958594/hadoop-for-human-genome-data

ADD REPLYlink written 4.2 years ago by Pierre Lindenbaum118k
I am sorry for the inconvenience. I will delete the other threads.
ADD REPLYlink written 4.2 years ago by shalini.ravishankar0

Cross posted on Quora http://qr.ae/6EsvP

ADD REPLYlink written 4.2 years ago by Matt Shirley8.9k
0
gravatar for Alex Reynolds
4.2 years ago by
Alex Reynolds27k
Seattle, WA USA
Alex Reynolds27k wrote:

You might start with Michael Hoffman's Genomedata paper, code and documentation.

ADD COMMENTlink written 4.2 years ago by Alex Reynolds27k
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1993 users visited in the last hour