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I loaded a BAM file and don see anything. Whats wrong?

April 26, 2017bam file loaded wrong

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I loaded a BAM file and don see anything. Whats wrong?

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Posted

The most common cause for this is a mismatch in chromosome names between the BAM file and the IGV genome it is being viewed against. If viewing against the supplied hg18 genome, for example, the chromosome names must be of the form chr1, chr2, etc. Many Bowtie users report this problem after aligning to the supplied NCBI index files because chromosomes are name by acession numbers of the form SN:gi|224589811|ref|NC_000002.11|.