Seqanswers Leaderboard Ad
Collapse
Announcement
Collapse
No announcement yet.
X
-
Under the contrib/extractContigReads directory in Velvet you'll find a script to do this
-
Velvet question
How can one extract all of the reads that were used in the assembly, in order to do the re-mapping step you described?
Leave a comment:
-
Hi Simon,
I'm not by any means an expert on this, but you probably have two options:
1. Convert the kmer coverage in the stats.txt file to base-coverage and use that as a proxy for expression level
2. Align the reads to the assembled transcripts using something like Bowtie and then extract the coverage of each transcript using SAMTools
Hope that helps!
Leave a comment:
-
Velvet/Oases transcript expression level?
Hi,
I am in the process of de novo transcriptome assembly from a non-model eukaryote. I have 17 million 65 bp, paired-end reads that I have assembled with Velvet and then Oases. This gives nice results in that I am getting full-length contigs that appear reasonable when compared to orthologues in related model eukaryotes. However, I am really after relative transcript expression levels. Does anyone know if there as a way that I can get information on that from this software combination?
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, Yesterday, 11:49 AM
|
0 responses
15 views
0 likes
|
Last Post
by seqadmin
Yesterday, 11:49 AM
|
||
Started by seqadmin, 04-24-2024, 08:47 AM
|
0 responses
16 views
0 likes
|
Last Post
by seqadmin
04-24-2024, 08:47 AM
|
||
Started by seqadmin, 04-11-2024, 12:08 PM
|
0 responses
61 views
0 likes
|
Last Post
by seqadmin
04-11-2024, 12:08 PM
|
||
Started by seqadmin, 04-10-2024, 10:19 PM
|
0 responses
60 views
0 likes
|
Last Post
by seqadmin
04-10-2024, 10:19 PM
|
Leave a comment: