I have n=3 samples of neuronal ribosome immuno-precipitated RNA seq data. All the data has more or less same alignment rate like below:
34167279 reads; of these: 34167279 (100.00%) were unpaired; of these: 22847962 (66.87%) aligned 0 times 7904836 (23.14%) aligned exactly 1 time 3414481 (9.99%) aligned >1 times 33.13% overall alignment rate
I checked those
(66.87%) aligned 0 times they are rRNAs. Looks like need to do more special rRNA depletion steps than given in the Takara Kit, as the sample has enriched Ribosome.
I have around 100 differentially expressed genes (FDR<0.05) but they don't make any sense to the experiment. PCA also didn't separate well. Anybody has suggestion about what percentage of rRNA contamination is acceptable? The number of reads aligned is enough to do differential expression?
Thanks for your help!