View Single Post
Old 05-02-2016, 03:35 AM   #11
Jane M
Senior Member
Location: Paris

Join Date: Aug 2011
Posts: 239

I wrote 2 posts last week, they do not appear (waiting for validation, I don't know why). I hope this one will be posted.

Originally Posted by GenoMax View Post
You can use the sequence of the human rDNA repeat found here to map against.
I ran two tests:
1) map the unmapped reads as previously, except I change the reference to rDNA fasta sequence.
Then, I got alignment rate of 83.2, 82, 81.6 and 74.8% for ribodepleted samples and 7, 4.4, 2.8 and 4% for polyA samples.

2) map the paired trimmed reads as previously, except I use as reference the rDNA fasta sequence.
Then, I got alignment rate of 24.3, 14.1, 18.1 and 13.3% for ribodepleted samples and 0.5, 0.2, 0.2 and 0.1% for polyA samples.

I read in some posts that 5% was low remaining rDNA sequence after ribodepletion. I have quite higher percentage. What is the classical range?

From these tests, I am convince that the different mapping rates I got between the two experiments come from the rDNA sequence still present in ribodepleted samples that are not reported in hg19.

Thank you for the help you provided me.
Jane M is offline   Reply With Quote