Tweet
Hello all,
For Solid RNASeq data, we are getting between 30% - 40% of total raw reads mapping uniquly, using the default parameters of tophat.
Quite a lot of reads don't map back at all (~50%) fail to align at all
.
Using bioscope, with the default parameters but instructing it to report 1 hit (not the same as unique I guess), we get approx. 60% of total raw reads mapping back.
This does not seem like a good return per sequencing run. I was wondering if I could get any feedback here on what percentage of usable reads (whatever you define that to be) other labs are getting per sequencing run.
Thanks for any feedback!
For Solid RNASeq data, we are getting between 30% - 40% of total raw reads mapping uniquly, using the default parameters of tophat.
Quite a lot of reads don't map back at all (~50%) fail to align at all
.Using bioscope, with the default parameters but instructing it to report 1 hit (not the same as unique I guess), we get approx. 60% of total raw reads mapping back.
This does not seem like a good return per sequencing run. I was wondering if I could get any feedback here on what percentage of usable reads (whatever you define that to be) other labs are getting per sequencing run.
Thanks for any feedback!