Hello, I was wondering with IDBA-Tran they want you to have a .fasta file as input. I converted my file from .fastq to .fasta but I noticed in their example conversion they also filter out reads with NNNs in them. How important is this for proper assembly of the transcriptome? Thanks.
Seqanswers Leaderboard Ad
Collapse
Announcement
Collapse
No announcement yet.
X
-
It is always an option to clean your reads of NNN and other low quality reads, but you don't need to, for this and other assemblers. De-novo assemblers do internally use higher quality reads instead of poor ones where available. I do both ways sometimes, but current Illumina sequencer outputs are generally high quality.
I get good transcript assemblies with idba-trans, with a caveat that I use all the kmer-set "transcripts-kk.fa" outputs, rather than IDBA's final "merged" set, which has poorer gene completeness than the per-kmer sets.
Find here a comparison of 4 gene assemblers, used in EvidentialGene's production of highly accurate gene reconstructions for the malaria mosquito and yellow fever/Zika mosquito:
idba_trans comes in second best, after velvet/oases the reigning champion of gene assembly. idba_trans uses less memory and runs faster than velvet/oases, and the authors' paper helps explain why it and velvet/oases do so well with multi-kmer constructions of the variably expressed genes and their alternate transcripts. Please consider using http://eugenes.org/EvidentialGene/ methods along with several gene assemblers to obtain highly accurate animal and plant gene sets.
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, Today, 11:49 AM
|
0 responses
12 views
0 likes
|
Last Post
by seqadmin
Today, 11:49 AM
|
||
Started by seqadmin, Yesterday, 08:47 AM
|
0 responses
16 views
0 likes
|
Last Post
by seqadmin
Yesterday, 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
|
Comment