Entering edit mode
7.9 years ago
yrc0313
•
0
Hi everyone,
I'm new to RNA-seq and was wondering if there is a generally accepted minimum mapped percent (hg19)? Right now I seem to be getting around 60-70%. Thank you!
Where is your sample coming from? Is there a possibility of contamination? If yes, from which source.
The samples are from patients and were checked for contamination with none found. Thank you for your help!
While the percentage can be much higher you have what you have. Are you using a splice-aware aligner? You can take a look at the reads that did not map by checking a few with blast @NCBI (unless you have already done this by "were checked for contamination").