Question: Pseudogenes masking during short-reads alignment
0
gravatar for hibernicah
4 days ago by
hibernicah10
hibernicah10 wrote:

Do you think that pseudogenes masking for short-reads mapping is sensible? I'm analysing ribosome profiling data that are about 25-32 nt long and even after standard pre-alignment to rRNA region I still see some multi mapping that maybe could be diminished if pseudogenes regions were hard-masked in the reference genome. For example, in this paper pseudogenes masking for ribosomal proteins has changed alignment substantially.

On the other hand as ~ 15% of pseudogenes is estimated to be transcribed, such masking could potentially introduce serious bias in quantification of those genes. What is your experience?

ADD COMMENTlink modified 4 days ago • written 4 days ago by hibernicah10
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1196 users visited in the last hour