I've seen 3'-5' coverage plots used to diagnose RNA degradation for RNA-Seq experiments. Before I begin writing my own I was just wondering if anyone knows of an existing script that can produce them (from a BAM and a GTF for instance)?
Seqanswers Leaderboard Ad
Collapse
Announcement
Collapse
No announcement yet.
X
-
-
Nice, thanks!
I was also interested in some easy way to get what the geneBody_coverage.py module is plotting.
Comment
-
Hi, have you tried ngs.plot? It is a very powerful and flexible tool to plot NGS samples. In addition to a global plot for the entire genome, you can create any combination of bam files and gene lists. You can plot RNA-seq or ChIP-seq which are implemented as two different modes.
As for your question, click this example .Last edited by asiangg; 06-19-2013, 09:42 AM.
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, Today, 07:03 AM
|
0 responses
10 views
0 likes
|
Last Post
by seqadmin
Today, 07:03 AM
|
||
Started by seqadmin, 05-10-2024, 06:35 AM
|
0 responses
31 views
0 likes
|
Last Post
by seqadmin
05-10-2024, 06:35 AM
|
||
Started by seqadmin, 05-09-2024, 02:46 PM
|
0 responses
41 views
0 likes
|
Last Post
by seqadmin
05-09-2024, 02:46 PM
|
||
Started by seqadmin, 05-07-2024, 06:57 AM
|
0 responses
33 views
0 likes
|
Last Post
by seqadmin
05-07-2024, 06:57 AM
|
Comment