Post Reply 
 
Thread Rating:
  • 0 Votes - 0 Average
  • 1
  • 2
  • 3
  • 4
  • 5
Are the reads filtered by quality?
14-Aug-2013, 10:14 AM
Post: #1
Are the reads filtered by quality?
In your pipeline I see that you pre-process the read removing the adaptor and removing rRNA sequences. However, did you filter the reads by its quality? And did you clip the first nucleotide from the reads prior to aligning?
Find all posts by this user
Quote this message in a reply
14-Aug-2013, 10:15 AM (This post was last modified: 14-Aug-2013 10:15 AM by audrey.)
Post: #2
RE: Are the reads filtered by quality?
We do not filter reads by quality per se. We use the RUM alignment tool (http://cbil.upenn.edu/RUM/userguide.php ) which in turn uses Bowtie with the -v option (up to 3 mismatches allowed) . Quality values tend to be lower at the 3' end of the read and if there are mismatches, they are clipped by RUM.
When you refer to removing the first nucleotide from the read, I presume you are referring to the possible untemplated addition during reverse transcription. We don't remove the first nucleotide as we allow up to 3 mismatches in the entire read. If the first nucleotide is a mismatch, then the read can still be aligned correctly.
Find all posts by this user
Quote this message in a reply
Post Reply 


Forum Jump:


User(s) browsing this thread: 1 Guest(s)

GWIPS-viz | Return to Top | Return to Content | Light (Archive) Mode | RSS Syndication