rRNA contamination in poly A-enriched libraries

Question

[seta]

Hi all,

I got Illumina data resulted from poly A-enriched libraries sequencing. I checked the probable rRNA contamination using SortMeRNA tool, there was 1.09% rRNA sequences. Before checking the rRNA contamination, I did transcriptome assembly and now I don't know if this contamination is significant or trivial. Could you please put your opinion about it, if the contamination is significant and I should make a new assembly with the clean (non-contaminated) data?

Thanks in advance

[GouthamAtla]

I think it depends on what do you want to do with the assembly. If they all form a few contigs, you could either remove them or ignore them. I don't know if it happens or not but if they are messing up the assembly by being a part of assembled transcripts from mRNA reads, you should remove them.

[seta]

Actually, I don't know what they do with assembly and if the 1% rRNA sequences is big for assembly!

Answer 1

[Fabio Marroni]

I think that 1% contamination from rRNA is not too bad. However, just to be sure, you could filter rRNA contaminants before the assembly. My colleagues developed a tool for doing this called ERNE-filter; I suggest you try that or some similar tool.