Bam loading error (sequence name does not match current genome) rat reference (rn5)

[Dash -]

Hi there,

 

Rat genome assembly 5.0 has been recently released and I mapped my reads to it recently and want to view them in IGV like the previous release. The new release genome called rn5 in IGV however when I tried to load my Bam file (no markduplication). I got an error saying does not contain any sequence names which match the current genome. Any suggestion of how to fix this ?

 

The IGV version is  IGV_2.1.30

Genome rn5

 

P.S i get the same error msg when I try the old reference rat genome rn4

 

Regards

[Jacob Silterra]

The BAM file you're loading is expected to have chromosome names which match those in the genome file. You can workaround this by creating an alias file, see the bottom of http://www.broadinstitute.org/software/igv/LoadData

-Jacob

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Jacob Silterra
Software Engineer
Broad Institute

[Jim Robinson]

Hi, to elaborate a little you will get that message if your sequence names don't match the genome you are using.  Execute the following with samtools to see the sequence names in the file

samtools view -H  <your bam file>

There will be a section with entries like this, in this example the sequence name is "chr1"

SN:chr1

Jim