I would anticipate that impact would be minor on the global scale but individual genes might be affected.
Longer reads improve alignment. False alignments could be reduced since longer reads are more unique.
In order to avoid mappability bias I would probabl trim all data to a constant length, for example with
and then remap.
The fact that both groups differ in sequencing implies that they might have been produced at different timepoints, is that the case? If so the experiment would be confounded, hopefully the confounding effect does not mask any meaningful biological effects. Can you elaborate?
modified 12 days ago
12 days ago by
ATpoint ♦ 44k