Post Reply 
 
Thread Rating:
  • 0 Votes - 0 Average
  • 1
  • 2
  • 3
  • 4
  • 5
Question regarding lack of correspondence between coverage plots and ribosome profile
20-Nov-2014, 04:37 PM
Post: #1
Question regarding lack of correspondence between coverage plots and ribosome profile
The following query from Chao may be of interest to other users of GWIPS-viz and so I am posting it here:


Chao sent us the attached file which shows that there is discrepancy between the coverage plot and ribosome profile for the Ingolia et al. 2009 yeast ribo-seq data and asked if ribosome profiles and coverage plots are generated based on THE SAME ALIGNMEMT results, we can rebuild the LEFTMOST part (around the start codon) of coverage plot from ribosome profile as in p.3 of attached before.


Response:

We want to thank Chao for bringing this to our attention.

We checked the original coverage alignment file for the region highlighted in Chao's attached file and noticed that some of the coverage reads in that region were <25nt. The RUM default minimum read length at the time we processed the Ingolia et al. 2009 data was 20nt. However, we used a minimum read length of 25nt for generating the ribosome profiles. Consequently there is not a direct correspondence between the coverage files and the ribosome profiles.

The Ingolia et al. 2009 dataset was one of the first ribo-seq datasets that we processed. For more recent datasets, we have added an input parameter for RUM specifying a minimum read length 25nt.


Attached File(s)
.pdf  scan001.pdf (Size: 389.05 KB / Downloads: 2)
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