Error Message; "Does not contain any sequence names which match the current genome."

[R. Churchill]

I am trying to upload files (BAM format) to compare them to my reference genome but I get the error message "does not contain any sequence names which match the current genome". It's worked before and then I updated Java and IGV and now I can't upload the genes I'm trying to examine. Does anyone know what I can do to fix this?  Thank you in advance!

[Jim Robinson]

Could you check the sequence names in your BAM header, and compare those to the sequence (chromosome or contig) names in your reference genome?

Jim

I am trying to upload files (BAM format) to compare them to my reference genome but I get the error message "does not contain any sequence names which match the current genome". It's worked before and then I updated Java and IGV and now I can't upload the genes I'm trying to examine. Does anyone know what I can do to fix this?  Thank you in advance!

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[R. Churchill]

Hi Jim,

(This is my first time using IGV so I am sorry)  They are things like A10_cat_sorted.bam.  And my chromosome numbers are just chr 1 etc.

Rebecca

[Jim Robinson]

No problem, so you're not seeing anything because A10_cat_sorted.bam doesn't match any chromosome names, so there is no way to know where to place it.   Do you have the fasta file the bams were aligned to?  If you do the "fix" is to load this first from the Genome menu (Load genome from file...),   then load your BAM.  

Jim

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[R. Churchill]

Tried that by going File>Load from File and it said to "Check the file extension". Is there something wrong with the file that I have been sent?

Rebecca

[Jim Robinson]

Rebeca, 

As I said, you load fasta files from the "Genome" menu,  not the "File menu.    I can't really say if there's something wrong with the file you were sent as I don't know what you are trying to do.   What organism have you sequenced?   That is a rather strange name for a sequence  (A10_cat_sorted.bam),  how are you determining the sequence names in your bam file? 

Jim

Tried that by going File>Load from File and it said to "Check the file extension". Is there something wrong with the file that I have been sent?

Rebecca

On Friday, December 5, 2014 11:10:49 PM UTC, Jim Robinson wrote:

No problem, so you're not seeing anything because A10_cat_sorted.bam doesn't match any chromosome names, so there is no way to know where to place it.   Do you have the fasta file the bams were aligned to?  If you do the "fix" is to load this first from the Genome menu (Load genome from file...),   then load your BAM.  

Jim

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