Dear colleagues Thanks in advance for your help I would like to assemble, de novo, a transcriptome from which I have two kind of data:
1) long reads (Illumina Roche GS FLX System, single-end reads ~400bp) 2) Short reads illumina ~40bp.
I have used already the long reads for the assembly but the results are poor I have used the short reads (using Trinity) and the assemble outputs are much better but I would like to use both data at the same time hoping to build a much better transcriptome. I could not manage it using Trinity. Could you please give me some hints how to use both long and short reads to assemble the transcripts? Best regards Roberto