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Old 05-21-2010, 10:23 PM   #1
zhouyi
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Location: Changsha, China

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Default problems about 454 transcription data analysis

Hi! Folks
Our group focus on transcription differentiation (sequence and expression copies) of different cyprinid fishes. Different samples were sequenced by company we commited (454), then they gave us the result.
As a freshman, i don't know how to analysis. I think i should blast the fasta sequences of "454Isotigs.fna". However, the data is so huge that maybe some software must be used. The most similar modle species is zebrafish (Danio rerio).
I wanna to know is the method which blast the sequence of "454Isotigs.fna". is correct and i wonder if there any software could be competent for the work.
Thank you guys!
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Old 05-22-2010, 02:53 PM   #2
cdragon
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You may need to read some transcriptome analysis papers and learn to write programs to analyze your data. Or just try to find a bioinformatics collaborator.
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Old 05-22-2010, 10:07 PM   #3
jiaco
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Go to the galaxy site: http://main.g2.bx.psu.edu/
and they have some nice intro movies about processing various data sets.

Blast is not a good first step if you have quality information in your data as there are many programs that will use that quality information during the alignment phase.
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Old 05-23-2010, 04:39 PM   #4
zhouyi
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Thank you, folks.
Although my problem is not resolved, i got a lot information. I am learning how to use galaxy. It's not easy for fresh man but i am trying.

Last edited by zhouyi; 05-24-2010 at 12:03 AM.
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