I met the situation of high % reads with multiple alignment sites. Our procedure is removing rRNA by Ribozero kit from ~1 microgram RNA isolated from rat liver tissue followed by standard RNA seq library construction. In some samples, we found a lot of reads, ~40-50%, has high similarity with rRNA and other ~20% reads with multiple alignment sites, of them most belong to 7sRNA.
We also checked bioanalyzer map of RNA after rRNA removal and found a ~140bp peak with with high FU value ~200. However we didn't check peaks around 18s and 28s positions in the map.
We speculated that the tissue has kind of specific features that Ribozero kit can't remove 7s RNA or SnRNA thus result in this multi-alignment situation.
Has this happened in your experiment? Could you give me some suggestion?
Many thanks,
Yuk
We also checked bioanalyzer map of RNA after rRNA removal and found a ~140bp peak with with high FU value ~200. However we didn't check peaks around 18s and 28s positions in the map.
We speculated that the tissue has kind of specific features that Ribozero kit can't remove 7s RNA or SnRNA thus result in this multi-alignment situation.
Has this happened in your experiment? Could you give me some suggestion?
Many thanks,
Yuk
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