I have been doing genome assembly with one pair-end library (insert length = 500) for a non-model plant species using Velvet. The assembly is very fragmented.
Since i also have pair-end RNAseq sequencing data, I am wondering if i can use RNAseq data to improve genome assembly.
My questions are: (1) Does it make sense to map transcriptome assembly to genome assembly and join genome scaffolds/contigs spanned by the same transcripts?
(2) can I try using RNAseq reads data for the same purpose? I mean using RNAseq reads as genomic sequence reads to do de novo assembly. Considering RNAseq PE reads are from alternatively spliced transcripts, I will use them as single-end reads when doing genome assembly.
I will appreciate it very much if someone can point out whether these ideas are reasonable or not or give me additional suggestions.