Blank tract when uploading bedgraph file

[Euan McDonnell]

Hi,

I've tried uploading the bedGraph file "bg_test.bedGraph" to IGV but every time I do I get a completely flat track - could it be due to the low number of reads per coordinate (averages 1-2). Wouldn't IGV at least scale the peaks relative to each other, even if they are overall small?

I am using IGV_2.4.5.

Thanks

Euan McDonnell

[Helga Thorvaldsdottir]

Hi Euan,

All the lines in the file have the chromosome value "chr" which is not a valid chromosome number.

Helga

[Euan McDonnell]

Hi Helga,

What would a correct chromosome value for MG1655 K12 be (or how would I go about finding this out)? I've tried it with NC_000913.3  too but this still doesn't work.

(apologies I'm very new to this)

Thanks,
Euan

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[Helga Thorvaldsdottir]

Euan,

The chromosome name needs to match a name in the currently loaded reference genome (either directly or via an alias file). If you loaded the genome via a FASTA file, you can see the names there. Or, once a genome has been loaded into IGV you can see the names in the chromosome dropdown menu. For example, IGV hosts two E. coli K-12 MG1655 genomes. I loaded one, and saw the chromosome name U00096.2 in the dropdown. I replaced the "chr" in the bedgraph file with "U00096.2" and the data shows up when the file is loaded. 

Helga