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Old 06-12-2013, 01:26 AM   #4
Devon Ryan
Location: Freiburg, Germany

Join Date: Jul 2011
Posts: 3,480

Originally Posted by vijesh View Post
can we put the two files as input in tophat.means that genome file in fasta and also the transcript file?
Sort of, I can read a few different meanings into what you wrote so I'll write some pseudo-commands just to ensure that my meaning is clear. Let us assume that your Cassava genome file is called "Cassava.fa" with an annotation file "Cassava.gtf", your virus genome file is called "Viruses.fa", and the transcripts whose origin you're interested in determining are in a file called "reads.fa". The work flow would then be something like the following:

cat Cassava.fa Viruses.fa > CombinedGenome.fa
bowtie2-build CombinedGenome.fa Combined
tophat -G Cassava.gtf Combined reads.fa
You can then see which reads originated from which chromosome/contig or whichever virus by using samtools view on the resulting accepted_hits.bam file (you'll probably want to filter out reads that map equally to both Cassava and viral genomes, for which you'll probably have to write a program).

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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