Can someone explain to me what the orientation in paired-end RNA-seq data means? Is forward/forward the standard orientation? How does this affect tophat options, just specify unstranded Rna-seq?
Seqanswers Leaderboard Ad
Collapse
Announcement
Collapse
No announcement yet.
X
-
If you are only looking for a primer on the "paired end" part have a look at this blog entry: http://www.homolog.us/blogs/blog/201...looking-reads/ You are less likely to have the second kind of libraries mentioned in the post.
Comment
-
Originally posted by puggie View PostWhat protocol did you use for library preparation? Normally for ScriptSeq Illumina libraries, the forward reads would correspond to the DNA coding strand while the reverse reads would be reverse complements,
Comment
-
I'm not sure what the 'standard orientation' is.
But if you want to know more about read-orientation then take a look at these threads:
Discussion of next-gen sequencing related bioinformatics: resources, algorithms, open source efforts, etc
And while 'unstranded' is the default mode for tophat/bowtie, you need to change that if your library is something else.
Comment
-
Originally posted by Nick View PostI'm looking at this SRA entry
http://www.ncbi.nlm.nih.gov/sra?term=SRX142112
Comment
Latest Articles
Collapse
-
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 -
-
by seqadmin
Proteins are often described as the workhorses of the cell, and identifying their sequences is key to understanding their role in biological processes and disease. Currently, the most common technique used to determine protein sequences is mass spectrometry. While still a valuable tool, mass spectrometry faces several limitations and requires a highly experienced scientist familiar with the equipment to operate it. Additionally, other proteomic methods, like affinity assays, are constrained...-
Channel: Articles
04-04-2024, 04:25 PM -
ad_right_rmr
Collapse
News
Collapse
Topics | Statistics | Last Post | ||
---|---|---|---|---|
Started by seqadmin, Today, 08:47 AM
|
0 responses
10 views
0 likes
|
Last Post
by seqadmin
Today, 08:47 AM
|
||
Started by seqadmin, 04-11-2024, 12:08 PM
|
0 responses
60 views
0 likes
|
Last Post
by seqadmin
04-11-2024, 12:08 PM
|
||
Started by seqadmin, 04-10-2024, 10:19 PM
|
0 responses
57 views
0 likes
|
Last Post
by seqadmin
04-10-2024, 10:19 PM
|
||
Started by seqadmin, 04-10-2024, 09:21 AM
|
0 responses
53 views
0 likes
|
Last Post
by seqadmin
04-10-2024, 09:21 AM
|
Comment