Hi, I am doing environmental metagenomics for microbes. A lot of time we have t o do 16S rRNA amplicon sequencing and metagenomics. The reason is WGS metagenomics can't yeild a lot of rRNA gene reads. For example, if you have 1 million of metagenomic reads, you will get ~ 1000 reads of rRNA gene. The rule of thumb is 1 of 1000. I remember someone told me the current technique difficulties. He also says WGS tends to generate more reads coding for housekeeping genes than normal funnctional genes? Can anyone explain why is this? I know like HiSeq will do a bridge amplification like PCR. Is it because the universal primers/adapters using in the bridge amplification are not specific ?
Seqanswers Leaderboard Ad
Collapse
Announcement
Collapse
No announcement yet.
X
-
It has nothing to do with bridge amplification. WGS is whole-genome sequencing. The rRNA cluster is ~4500bp long, and a typical microbial genome is ~1000X as long. So only 1/1000 reads contain rRNA sequence. [Note: these are very rough size estimates and don't account for repeats of the rRNA genes, but it's a reasonable heuristic.]
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
25 views
0 likes
|
Last Post
by seqadmin
04-11-2024, 12:08 PM
|
||
Started by seqadmin, 04-10-2024, 10:19 PM
|
0 responses
27 views
0 likes
|
Last Post
by seqadmin
04-10-2024, 10:19 PM
|
||
Started by seqadmin, 04-10-2024, 09:21 AM
|
0 responses
24 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