Reassembling Transcriptome Using Recently Published Genome

Question

[Raghul]

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. I have compared some of our assembled transcripts with available complete CDS & I found the assembled transcript query coverage was not more than 60%. So I felt "reference assembly" could increase the "query coverage" than the "de novo assembly". 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 ?

Based on the previous answers posted here I have intended to to check out Cufflinks & Scripture, anyway I need suggestions that could help do things better!

Supplementary question-Since I have only single transcriptome, is it possible to do statistical analysis for Gene Ontology results ?, because in this case the GO results will be based on available "contig count" !

thank you

raghul

Answer 1

[JC]

You can convert your files to FastQ format, just combine the fna and qual files (there are some scripts if you don't know/want to code). The fastq file is required for many aligners, you can try Bowtie2 or BWA.

With one sample is hard (impossible?) to obtain confident analysis, your statistics will be bad.