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?
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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.
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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.
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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.
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