Hi all,

I have a single-end dataset squenced the 3'end of mRNA. The library is constructed so that only the end away from polyA tail is seuqenced. We want to sequence the 3'UTR region as much as possible, but it has inevitablely sequenced the coding regions as well. The ultimate goal is to call variants from this dataset. Since there is no reference for this plant species, I now try to assemble the reads into concensus. Although it is RNAseq, I wonder maybe it is better to use genome assembler to do the task since most transcriptome assemblers focus on alternative splicing problem and I assume my dataset have fewer issue from this aspect. Do you have any recomemdations or suggestions for this? Thank you very much!