RNA-seq assembly and reference genome

[lfaino]

Dear community,
I have a question.
I have an RNA-seq by Illumina pair ends. I have a reference genome and transcriptome. My question is if there is any software that I can use to map the RNA-seq reads on the reference transcriptome and retrieve the assembled transcriptome based on my sequences. I want this because my coverage is low and in this way I can use a known reference to get better information about my transcriptome too.

Regards
Luigi

[harrike]

commercial software: CLC genome workbench. www.clcbio.com. It is quite expensive.

There are many free software shared in this community. You'd better use "search" to get what you want.

[Thorondor]

actually it is not that easy, there are many assemblers around but they mostly require a genome as reference and not a transcriptome. I also checked for assemblers where you can give a transcriptome of a near relative as reference but didn't found anything. :-(

You maybe can "fake" the transcriptome as genome, but I don't know if this will work.

If you want to use your genome as reference you could try cufflinks.

[ksc]

I am using BWA to remap mRNAseq data to a reference transcriptome and samtools to call the consensus of the remapped transcriptome. I have also used CLC for this purpose, as suggested by harrike. I have not yet used paired-end data, but I believe both packages can handle paired-end data.