Hello,
i searched in the forum but did not found a clear answer.
I have a certain number of bacteria RNA samples that were sequenced using an illumina paired end approach. The library construction illumina total RNA + ribodepletion were performed by the sequencing provider. By using FastQC and sortMeRNA I found that all datasets are contaminated with rRNA to different %. Some datasets have 1%, while others have 10%, 20% and some even 50%! I understand that there was an obvious problem with the rRNA depletion. Still, I have more than 20M reads mapping to transcripts, in principle 5M reads are sufficient for DEG analysis in bacteria. My questions are:
These datasets could be still be used for DEG analysis if i remove the rRNA reads ? In general how much rRNA contamination is tolerated ? Is there something published in the litterature about rRNA contamination issue for DEG analysis?
thank you very much
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schelarina •
Your question has been answered before: What % of rRNA contamination is acceptable?
10% of contamination is acceptable according to what discussed, but there is no article or study really reporting this threshold, and this is what I would like to find.
the number of reads that do not align to rRNA go from a minimum of 6M to a maximum of 45M and about 95-97% of them align to mRNA.
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there is no need to remove the rRNA reads.
Map your reads against the reference genome and get a gene count
table
Remove the rRNA genes from the gene count table