Hi all, I'm trying to figure out a good pipeline for a de novo metatranscriptomics project on soil and rhizosphere samples. I'm looking into the Khmer protocols which use Trinity, but I wonder if there are other good pipelines or scripts around for this purpose. Any advice is welcome !
Seqanswers Leaderboard Ad
Collapse
Announcement
Collapse
No announcement yet.
X
-
de novo metatranscriptomics
Originally posted by stevebaeyen View PostHi all, I'm trying to figure out a good pipeline for a de novo metatranscriptomics project on soil and rhizosphere samples. I'm looking into the Khmer protocols which use Trinity, but I wonder if there are other good pipelines or scripts around for this purpose. Any advice is welcome !
-
Hi, I just found a list of tools on this webpage (http://www.metagenomics.wiki/pdf/def...ranscriptomics). Personally I only used Kraken so far, but actually Kraken only assigns taxonomic units to reads and not functional or genexpression stuff like rpkm. But maybe one of the other tools might be of some interest.
Kallisto - RNA-seq transcript abundance estimation
Kraken - assigns taxonomic labels to short sequencing reads
HUMAnN2 - community-wide gene transcription and pathway analysis
requires pairs of DNA and RNA sequencing of the same biological sample
PanPhlAn - strain-specific transcriptomics analysis
requires pairs of DNA and RNA sequencing of the same biological sample
Maybe it could also be worth to have a look at MetaTrans, MEGAN,COMAN or SAMSA.
Comment
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
24 views
0 likes
|
Last Post
by seqadmin
04-11-2024, 12:08 PM
|
||
Started by seqadmin, 04-10-2024, 10:19 PM
|
0 responses
25 views
0 likes
|
Last Post
by seqadmin
04-10-2024, 10:19 PM
|
||
Started by seqadmin, 04-10-2024, 09:21 AM
|
0 responses
21 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