I have used paired end sequences for RNA-Seq experiments in the past with the understanding that PE reads are 'more accurate' somehow. One paper that I found says that the false positive rate is lower with PE. Single reads are a lot less expensive and I may be able to afford to sequence the libraries deeper. What do others on this forum use? PE or SE for rna-seq?
Seqanswers Leaderboard Ad
Collapse
Announcement
Collapse
No announcement yet.
X
-
I would always recommend PE for anything other than quantification studies. For quantification, it depends. But otherwise - per base, PE should always be cheaper than SE, and give massive advantages for accuracy.
This:
Single reads are a lot less expensive and I may be able to afford to sequence the libraries deeper.
So, it depends on the goal of your RNA-seq experiment! If you want to identify isoforms, or want maximal specificity, absolutely you should do PE. If you are just interested in differential expression of genes in general and don't care which isoforms are expressed, then SE will be more cost-effective.
Comment
-
Sorry, may be a bit off-topic. I personally use PE libraries, but just recently found the issue with read-through (when forward and reverse reads overlap completely). The question is - to drop reverse ones or leave them? Could it bias coverage and downstream DE analysis? If drop, then how to deal with less overlapped pairs? Ideally I would like to preserve non-overlapped fragments only, but not sure if there is a software capable for...
Comment
Latest Articles
Collapse
-
by seqadmin
Despite advancements in sequencing platforms and related sample preparation technologies, certain sample types continue to present significant challenges that can compromise sequencing results. Pedro Echave, Senior Manager of the Global Business Segment at Revvity, explained that the success of a sequencing experiment ultimately depends on the amount and integrity of the nucleic acid template (RNA or DNA) obtained from a sample. “The better the quality of the nucleic acid isolated...-
Channel: Articles
03-22-2024, 06:39 AM -
-
by seqadmin
The field of conservation genomics centers on applying genomics technologies in support of conservation efforts and the preservation of biodiversity. This article features interviews with two researchers who showcase their innovative work and highlight the current state and future of conservation genomics.
Avian Conservation
Matthew DeSaix, a recent doctoral graduate from Kristen Ruegg’s lab at The University of Colorado, shared that most of his research...-
Channel: Articles
03-08-2024, 10:41 AM -
ad_right_rmr
Collapse
News
Collapse
Topics | Statistics | Last Post | ||
---|---|---|---|---|
Started by seqadmin, Yesterday, 06:37 PM
|
0 responses
10 views
0 likes
|
Last Post
by seqadmin
Yesterday, 06:37 PM
|
||
Started by seqadmin, Yesterday, 06:07 PM
|
0 responses
9 views
0 likes
|
Last Post
by seqadmin
Yesterday, 06:07 PM
|
||
Started by seqadmin, 03-22-2024, 10:03 AM
|
0 responses
51 views
0 likes
|
Last Post
by seqadmin
03-22-2024, 10:03 AM
|
||
Started by seqadmin, 03-21-2024, 07:32 AM
|
0 responses
67 views
0 likes
|
Last Post
by seqadmin
03-21-2024, 07:32 AM
|
Comment