Entering edit mode
6.7 years ago
t2g4free
•
0
I have different RNA-seq data, but there length is not the same length. I have learn the length have some influence on the following analysis, eg. DE analysis. And here comes the question, what should I do at this situation. Thx.
Since the two read lengths likely came from different libraries, I would be concerned about mixing and matching. Can you provide more context?
It's important to figure out how you got these different read lengths, so perhaps you could elaborate on the preprocessing steps you performed (filtering, trimming,...).
If the libraries were prepared with the same kit and sequenced on the same type of sequencer then there is no reason to be alarmed.
I'm trying to figure out the best method to extract DEG sets under a disease condition in mice. I have two control samples and three treated samples generated from two different sequencing chemistries. First four samples were sequenced with Illumina NextSeq 500 and the last one was sequenced with Illumina HiSeq2500. The read coverage and read length are in the table below. My question is how to get over with the variations introduced by two sequencing chemistries and read length differences to extract DEG under disease condition. Are there any suggestions?