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Old 06-07-2012, 07:47 AM   #1
dhanapala
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Cool Downstream analysis with Single end and Paired end with Hiseq

Hi

Which would be right online tool/platform to work with single end reads/pair end reads from Hiseq (50bp or 100bp) for the Soybean ?
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Old 06-07-2012, 09:00 PM   #2
samanta
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Quote:
Originally Posted by dhanapala View Post
Hi

Which would be right online tool/platform to work with single end reads/pair end reads from Hiseq (50bp or 100bp) for the Soybean ?
What do you mean by 'online tool'? Are you going to install a program and run on your computer, or do you expect to upload data somewhere and get it all done by a web-server?
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Old 06-08-2012, 05:56 AM   #3
dhanapala
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Hi

I am talking about is there a program which i can install in to my computer and work on.
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Old 06-08-2012, 07:48 AM   #4
samanta
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Originally Posted by dhanapala View Post
Hi

I am talking about is there a program which i can install in to my computer and work on.
Dhanapal,

There is too little information on what kind of reads you have and what you are trying to achieve, but given that a genome already exists for soybean, you will most likely need Bowtie-Tophat-Cufflinks and Samtools.


Best,
Manoj
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Old 06-08-2012, 10:08 AM   #5
dhanapala
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Smile Galaxy Server !

Hi

If i would like to use online server like Galaxy to analyze my RNAseq data from Soybean (Reference sequence available)

How many million reads can be loaded ?

What should be my PC configuration ?
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