Bedgraph problem in igv 2.2

[tesfalem rezene]

Hi,

I'm new to using the igv but recently i have  data (bedgraph) to analyze using igv (2.2). 

But, after opening the bedgraph file onto the igv, I don't see anything.

The chromosome name in the IGV 2.2 that i'm using is NC_000913.2 in the bedgraph however it's written as MG1655

I tried to change the chromosome name in my bedgraph into NC_000913.2 but even with that change, I don't see anything in the igv

I read from this group's post that i need to sort and index the bedgraph using IGV tools, i tried to do that but  it says error:null (unknown file type or sorting not supported) 

So, can anybody please help me fix this

attached is igv log and part of my bedgraph files that I copied into word doc

Thanks

TR

[Jacob Silterra]

I've opened your test snippet with IGV without issue. Remember that the extension needs to be .bedgraph, this is how IGV identifies files. Could you post a screenshot of what you do see when opening this file?

Thanks,

-Jacob

On Tue, Jan 15, 2013 at 1:04 PM, tesfalem rezene <tesf...@yahoo.com> wrote:

NC_000913.2

--
Jacob Silterra
Software Engineer
Broad Institute

[tesf...@yahoo.com]

Hi Jacob,

Thanks for the quick reply!

Attached is what i see when I open the file

[Jacob Silterra]

All of the features in your file are at the very beginning of the chromosome. Try zooming in to the region of interest (evidently 1-50). See http://www.broadinstitute.org/software/igv/Navigate

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[tesf...@yahoo.com]

Thanks Jaco!

I tried to do that but my data is actually for the whole genome and still not being able to see any thing on igv

Can you please send me what you got when opening my file

do i have to change anything other than the chromosome name from MG1655 to NC_000913.2?

Thanks a lot!

[tesf...@yahoo.com]

I can also send you the whole file

[Jacob Silterra]

This discussion was continued outside the list, the end result was that the user wanted to view both a bedgraph and bam file with chromosome names not matching those in the genome. The chromosome names can be resolved by using an alias file is described in http://www.broadinstitute.org/software/igv/LoadData/#aliasfile. The BAM file needed to be indexed by samtools; http://samtools.sourceforge.net/.

-Jacob