RNA-seq assembly

[lfaino]

Dear All,
I did an RNA-seq by using Illumina and now i would like to assemble it. I already used velvet and I got some nice results. However the assembly is not good enough. In NCBI there are some related species that are sequenced and I could give a try in assemble the RNA-seq data with these genomes. Can you suggest some software that I can use? As a input file, I have a FASTQ file.

Thanks

Luigi

[edge]

Hi Ifaino,

I'm dealing with RNA-seq as well.
Can I know how you identify whether the assemble result is good or not?
I'm plan to use MIRA for my RNA-seq de novo assembly.
Thanks for your sharing.

[lfaino]

Hi edge,
I know because a lot of assembled transcripts are not complete when I BLAST them against genomes of related species. Just for this. And for this reason. I would like to assemble my transcriptome against a reference genome.

Luigi