From: "DeQuincy Prescott (UCL)" <smgxdqc@live.ucl.ac.uk>

Subject: visualisation of a bam file

Date: 6 March 2012 19:03:23 GMT

To: <galaxy-user@bx.psu.edu>

Cc: Jennifer Jackson <jen@bx.psu.edu>

One of the concerns I am trying to resolve is that I have a bam file which I am trying to visualise on galaxy.

http://main.g2.bx.psu.edu/u/dqnc/h/unnamed-history

I was hoping to visualise the data here in Trackster (http://main.g2.bx.psu.edu/visualization/list)

But it doesn't seem to render. 

I have used "Reference genome build (dbkey): Human Feb. 2009 (GRCh37/hg19) (hg19)"

 

But get "no data for this chrom/contig." as a display message.

The original data is http://qnctv.com/science/chr22hg19.bam (55MB)

Ultimately we would like to be able to get a VCF file or even better still an essential changes file where known SNPs have been filtered out and any polymorphism have been checked for possible changes to amino acid sequence.

I am new to Galaxy and still exploring what it can do so correct me if it can't perform what I would like it to do.

Thank you for any help you can provide.

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DeQuincy Prescott

Sen Res Tech to Professor Bhattacharya

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