I am trying assemble transcriptome data from a Tubificinae annelid, genus Limnodrilus. I sent in tissue and eukaryotic RNA seq was run successfully (poly-A tail RNAs). However, the genomes I submitted for assembling the transcripts failed. I assume that they were not closely related enough. My primary interest is with hemoglobin transcripts, so I sent in all Hb transcripts I could find that were in the same family, but they also failed to assemble any transcripts. The company will charge an additional $600 to do de novo assembly, but I have little to no budget remaining. I understand that de novo assembly can be run on Geneious. Does anyone have experience with that kind of assembly for an organisms with no closely-related genome data? If so, is it a complex process, or just a push of a button, like it sounds? Alternatively, does anyone know of whole genome data or Hb transcript data from a worm closely related to Limnodrilus? Thanks!!!
Did you do trimming and quality control before assembly? There is a useful article with basic steps (they can be done in Geneious but tools like Trinity might work better).Article A simple guide to de novo transcriptome assembly and annotation
Ankur Das and Dominika Kadlečková
Thanks for the replies and helpful comments.
1) I may give Trinity a try. I'm a novice at this, though, so hope the learning curve is not too steep.
2) CD Genomics did QC, trimming, filtering. I have not yet received the raw data from them. Thanks for the article. Any more tips for a novice?
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