i have a fasta file containing all the virus genome which will affect cassava. i have transcript file also in fasta. in transcript file each transcript have 100 nucleotide length. I want to know whether these transcripts are inside the virus genom. any one help me pls?
Seqanswers Leaderboard Ad
Collapse
Announcement
Collapse
No announcement yet.
X
-
One relatively straight-forward way to attack this problem would be to make a combined fasta file for the viral genomes and cassava and then map the transcripts/transcript fragments against it. You can then get an idea how likely each fragment is to come from the host or virus. I assume that tophat or something like that would be an appropriate aligner, since presumably you have a mixture of host (i.e. spliced) and viral (I assume transcripts would be single exon, but I've only made viruses, not studied them) reads and not doing so might bias things.
I should note that I've never done what you're trying to do, but if no one replies with a better idea then this is enough to get you started.
-
doubt regarding tophat
Originally posted by dpryan View PostOne relatively straight-forward way to attack this problem would be to make a combined fasta file for the viral genomes and cassava and then map the transcripts/transcript fragments against it. You can then get an idea how likely each fragment is to come from the host or virus. I assume that tophat or something like that would be an appropriate aligner, since presumably you have a mixture of host (i.e. spliced) and viral (I assume transcripts would be single exon, but I've only made viruses, not studied them) reads and not doing so might bias things.
I should note that I've never done what you're trying to do, but if no one replies with a better idea then this is enough to get you started.
Comment
-
Originally posted by vijesh View Postcan we put the two files as input in tophat.means that genome file in fasta and also the transcript file?
Code:cat Cassava.fa Viruses.fa > CombinedGenome.fa bowtie2-build CombinedGenome.fa Combined tophat -G Cassava.gtf Combined reads.fa
It would be good to compare the results with and without using the GTF annotation, off-hand I'm not entirely sure how or if that might bias things.
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