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Problem Viewing Alignments in IGV When Loading Custom FASTA file

IGV provides a number of genomes that are hosted for example Human hg18. When you load this data the default is set to view the whole genome; you can zoom in to a chromosome from the drop-down menu to zoom to it.

I have assembled a Transcriptome into a FAST file and loaded it into IGV. However, my drop-down menu only lists sequences not the entire transcriptome (for example it shows c8_g1_i1,...,c56277_g1_i1).

Is there a way to get a whole genome/transcriptome view (see pressing "Home" button https://www.broadinstitute.org/igv/Navigate) for custom created FASTA files?

rna-seq rna-seq igv alignment
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updated by h.mon h.mon • written by moldach moldach

1 answer

I may be wrong (never tried to do this), but I think you need to create a genome file, as per instructions here.

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written by h.mon h.mon

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