Question: rRNA contamination in poly A-enriched libraries
3
gravatar for seta
3.8 years ago by
seta1.1k
Sweden
seta1.1k wrote:

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,

 

ADD COMMENTlink modified 3.7 years ago by Fabio Marroni2.2k • written 3.8 years ago by seta1.1k

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. 

ADD REPLYlink written 3.8 years ago by geek_y9.6k

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

ADD REPLYlink written 3.8 years ago by seta1.1k
1
gravatar for Fabio Marroni
3.7 years ago by
Fabio Marroni2.2k
Italy
Fabio Marroni2.2k wrote:

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. 

 

ADD COMMENTlink written 3.7 years ago by Fabio Marroni2.2k
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