We just had our first sequencing run performed on Hi-Seq.
We have done RNA-Seq experiment and it turned out that our libraries were heavily duplicated. The level of duplications varied from 35% up to 90%!
Somebody mentioned that can be due to library saturation when working with a small transcriptome or it can be PCR overamplification.
I don't think it's due to PCR but rather due to relatively small transcriptome we are dealing with (Arabidopsis) - but still 90%?
Have you seen such high level of duplications before? Is there any alternative reason for that?
The other question is: if this is due to library saturation how can we avoid that in future runs?
We have done RNA-Seq experiment and it turned out that our libraries were heavily duplicated. The level of duplications varied from 35% up to 90%!
Somebody mentioned that can be due to library saturation when working with a small transcriptome or it can be PCR overamplification.
I don't think it's due to PCR but rather due to relatively small transcriptome we are dealing with (Arabidopsis) - but still 90%?
Have you seen such high level of duplications before? Is there any alternative reason for that?
The other question is: if this is due to library saturation how can we avoid that in future runs?
Comment