Reassembling transcriptome using recently published genome

[raghulrajan]

Hi all,

I have 454 Roche transcriptome assembly results. It is a single transcriptome. It is assembled "de novo". Much recently a very closely related genome was published. So I want to reassemble with this new genome as "reference". I have 2 folders in the output file given to us by the company, they are 'sff' and "assembly". I cannot find a fastq file. Do I really need fastq file for assembling? I have .qual, .fna &. ace files. Are these files along with "new genome" enough for re-assembly ?

thank u
raghul

[mastal]

RReassembling transcriptome using recently published genome

The sff files should have all the info you need - you can extract the fasta and qual values from the sff file.

The format to use will depend on the assembler you choose, and what formats it accepts as input.