Hello all,
I have spent the last several months constructing 48 libraries for RNA sequencing from developing stingray tissue, which I am hoping to sequence on a HiSeq 4000 with 100 bp PE reads.
I have been as consistent as possible throughout my library preps, but I still ended up with a range of fragment sizes after size selection (median size range from 294-485). Further, each library has a fairly broad size distribution. I've attached BioAnalyzer traces for ~ 40 of the samples.
Will these libraries be comparable enough to detect differential gene expression among them? Alternatively, are there bioinformatics tools available that can account for batch effects during processing? Fragmentation is supposed to be random, and the fragment size differences occur across treatments i.e. each treatment has replicates with both shorter and longer fragments.
Thank-you in advance for any feedback!
- John
I have spent the last several months constructing 48 libraries for RNA sequencing from developing stingray tissue, which I am hoping to sequence on a HiSeq 4000 with 100 bp PE reads.
I have been as consistent as possible throughout my library preps, but I still ended up with a range of fragment sizes after size selection (median size range from 294-485). Further, each library has a fairly broad size distribution. I've attached BioAnalyzer traces for ~ 40 of the samples.
Will these libraries be comparable enough to detect differential gene expression among them? Alternatively, are there bioinformatics tools available that can account for batch effects during processing? Fragmentation is supposed to be random, and the fragment size differences occur across treatments i.e. each treatment has replicates with both shorter and longer fragments.
Thank-you in advance for any feedback!
- John
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