Originally posted by kmcarr
View Post
Seqanswers Leaderboard Ad
Collapse
Announcement
Collapse
No announcement yet.
X
-
Originally posted by cement_head View PostNope - You've misinterpreted the paper. It doesn't actually say that - it says that using the USS alone is problematic - but the combination of USS and STL is not.
Second, they failed to present any data demonstrating significant levels of PCR duplication in the data in the first place. What is needed in Fig. 5 is a curve plotting number of reads mapped for each of the 24 ERCC controls or mRNAs with out first doing any de-duplication by either USS alone or USS+STL. Only if that curve was significantly higher than the USS+STL curve (blue line in Fig. 5) could they make for adding molecular indexes to RNA-Seq libraries.
What the white paper is attempting to do is to sell a solution without first demonstrating a problem which needs solving.
Comment
-
Originally posted by kmcarr View PostI stand by my statements. USS would be problematic if duplicate removal was standard practice for RNA-Seq data. It is not.
Second, they failed to present any data demonstrating significant levels of PCR duplication in the data in the first place. What is needed in Fig. 5 is a curve plotting number of reads mapped for each of the 24 ERCC controls or mRNAs with out first doing any de-duplication by either USS alone or USS+STL. Only if that curve was significantly higher than the USS+STL curve (blue line in Fig. 5) could they make for adding molecular indexes to RNA-Seq libraries.
What the white paper is attempting to do is to sell a solution without first demonstrating a problem which needs solving.
Here is a link to example data that demonstrates the difference between USS usage and USS + STLs usage: http://www.biooscientific.com/Portal...lar-Labels.pdf
I hope this clears up your queries.
Regards,
Andor
Comment
Latest Articles
Collapse
-
by seqadmin
The sequencing world is rapidly changing due to declining costs, enhanced accuracies, and the advent of newer, cutting-edge instruments. Equally important to these developments are improvements in sequencing analysis, a process that converts vast amounts of raw data into a comprehensible and meaningful form. This complex task requires expertise and the right analysis tools. In this article, we highlight the progress and innovation in sequencing analysis by reviewing several of the...-
Channel: Articles
05-06-2024, 07:48 AM -
-
by seqadmin
The field of epigenetics has traditionally concentrated more on DNA and how changes like methylation and phosphorylation of histones impact gene expression and regulation. However, our increased understanding of RNA modifications and their importance in cellular processes has led to a rise in epitranscriptomics research. “Epitranscriptomics brings together the concepts of epigenetics and gene expression,” explained Adrien Leger, PhD, Principal Research Scientist...-
Channel: Articles
04-22-2024, 07:01 AM -
ad_right_rmr
Collapse
News
Collapse
Topics | Statistics | Last Post | ||
---|---|---|---|---|
Started by seqadmin, Yesterday, 06:57 AM
|
0 responses
12 views
0 likes
|
Last Post
by seqadmin
Yesterday, 06:57 AM
|
||
Started by seqadmin, 05-06-2024, 07:17 AM
|
0 responses
16 views
0 likes
|
Last Post
by seqadmin
05-06-2024, 07:17 AM
|
||
Started by seqadmin, 05-02-2024, 08:06 AM
|
0 responses
21 views
0 likes
|
Last Post
by seqadmin
05-02-2024, 08:06 AM
|
||
Started by seqadmin, 04-30-2024, 12:17 PM
|
0 responses
24 views
0 likes
|
Last Post
by seqadmin
04-30-2024, 12:17 PM
|
Comment