Downstream analysis with Single end and Paired end with Hiseq

dhanapala · 06-07-2012, 07:47 AM

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 ?

samanta · 06-07-2012, 09:00 PM

Quote:

Originally Posted by dhanapala

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?

dhanapala · 06-08-2012, 05:56 AM

Hi

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

samanta · 06-08-2012, 07:48 AM

Quote:

Originally Posted by dhanapala

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

dhanapala · 06-08-2012, 10:08 AM

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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06-07-2012, 07:47 AM	#1
dhanapala Junior Member Location: Columbia, MO, USA Join Date: Nov 2011 Posts: 8	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 ?

06-08-2012, 10:08 AM	#5
dhanapala Junior Member Location: Columbia, MO, USA Join Date: Nov 2011 Posts: 8	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 ?

06-08-2012, 05:56 AM	#3
dhanapala Junior Member Location: Columbia, MO, USA Join Date: Nov 2011 Posts: 8	Hi I am talking about is there a program which i can install in to my computer and work on.