hi, i met a problem, I hava two samples,the two samples are the same species, they have a similarity of 90%,the two samples are assembled by trinity respectively, I got more than 60000,50000 unigenes respectively. i used cd-hit to remove redundancy and tgicl to cluster unigenes.i got 90000 unigenes, most unigenes are not clustered. i blast two samples, the mapped result is 75%. why most unigenes are not clustered?
Seqanswers Leaderboard Ad
Collapse
Announcement
Collapse
No announcement yet.
X
-
Originally posted by smm View Posthi, i met a problem, I hava two samples,the two samples are the same species, they have a similarity of 90%
Please take the time and effort to use proper spelling and grammar to clearly state what you wish to accomplish, what you have done, and what you have measured, before you post here. It is, of course, possible that you are looking at two samples of the same species, but your analysis was incorrect or your description was wrong. It's impossible to diagnose problems if you are not extremely specific. If you are talking about overlap between assembled transcriptomes, or whatever, you need to clearly state how it was calculated, and what kind of data you used. Transcriptome assembly is highly subjective and cannot trivially be used to determine whether pairs are the same species. Considering that you never used the term "RNA" anywhere in your query, it's hard to even tell what your data is or whether you are using it correctly.Last edited by Brian Bushnell; 01-25-2016, 08:36 PM.
Latest Articles
Collapse
-
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 -
-
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 -
ad_right_rmr
Collapse
News
Collapse
Topics | Statistics | Last Post | ||
---|---|---|---|---|
Started by seqadmin, 04-11-2024, 12:08 PM
|
0 responses
29 views
0 likes
|
Last Post
by seqadmin
04-11-2024, 12:08 PM
|
||
Started by seqadmin, 04-10-2024, 10:19 PM
|
0 responses
31 views
0 likes
|
Last Post
by seqadmin
04-10-2024, 10:19 PM
|
||
Started by seqadmin, 04-10-2024, 09:21 AM
|
0 responses
28 views
0 likes
|
Last Post
by seqadmin
04-10-2024, 09:21 AM
|
||
Started by seqadmin, 04-04-2024, 09:00 AM
|
0 responses
52 views
0 likes
|
Last Post
by seqadmin
04-04-2024, 09:00 AM
|
Comment