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Old 03-12-2020, 04:40 AM   #1
Junior Member
Location: Europe

Join Date: Mar 2020
Posts: 6
Unhappy inexplicable rRNA content

Hi guys,

long time reader, first time poster here. So here's my problem:

Did two RNAseq runs (NextSeq500, RNA Access Illumina prep, 20 samples per run).

The first run had 20 samples, high quality RNA, column based extraction Qiagen and showed 2-10% rRNA/sample (mapped with BWA, fasta from with search term txid9606[Organism:exp], then used samtools flagstat to find mapped reads).

The second run contained 10 samples high quality RNA, same extraction as first run and 10 samples RNA from FFPE samples, extracted with bead based Promega technology. rRNA content ranged from 4-38% and was not associated with RNA extraction method or quality (so low and high rRNA contents in both types of samples, in total 14/20 samples with >10% rRNA).

Does anyone have an explanation as to why my second run contains much more rRNA?

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