igv visualization

[kaps]

Dear all,
I have used bowtie2 to align paired – end illumina reads from cowpea and generated bam files. my next task is to visualise the alignments using igv. how do i proceed without a cowpea enome. My interest is to find out the proportion (number or percentages) of reads a matching each of the virus hits.
I am working on a server.

[dpryan]

You aligned the reads to something, so that thing is your reference genome.

[GenoMax]

@kaps: As Devon has already pointed out, your "reference" in this case is the fasta format genome file that you used to create your aligner indexes. You can't identify the "virus" hits unless you know (from an annotation source e.g. a GTF file) where the "virus" is in this reference genome file.

Where did you get your reference genome from? Perhaps there is an annotation file available there.

[kaps]

Hello,
For the aligner indexes (reference genomes) I used multi-fasta files downloaded from NCBI.

[GenoMax]

Then that multi-fasta file is your "reference" genome for IGV. You can import that file using the directions under section "loading a genome" here: http://www.broadinstitute.org/igv/LoadGenome