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Old 08-25-2012, 06:59 PM   #1
eavila
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Default Analysis transcriptome 454 + sanger

Hi all

I'm starting a transcriptome analysis using data from 454 and Sanger. I want to create a reference transcriptome (no genome information), what do you recommend me? Assemble data separately and then assemble the contigs or try a hybrid assembly.

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Old 08-25-2012, 10:31 PM   #2
Torst
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The 454 assembler (Newbler) can accept use extra Sanger reads in the assembly. You just need to ensure you put the correct headers in the .fasta/.qual files (eg. "template=XXXX dir=X library=XXX"). Don't forget to run it in "cDNA" assembly mode too.
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Old 08-27-2012, 09:59 AM   #3
eavila
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Thanks

I've tried with similar percentages of 90 and 95%, but only 67% of the sequences are assembled, i'll try moving some parameters to increase the number of reads assembled.
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