Test of forward email. ----------------------------------------------------- DeQuincy Prescott Sen Res Tech to Professor Bhattacharya ----------------------------------- about our group http://tinyurl.com/3264vn ------------------------------------ Mobile: +44 (0) 7590 695 435 Office: +44 (0) 207 608 6951 ----------------------------------------------------- Begin forwarded message:
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.
----------------------------------------------------- DeQuincy Prescott Sen Res Tech to Professor Bhattacharya ----------------------------------- about our group http://tinyurl.com/3264vn ------------------------------------ Mobile: +44 (0) 7590 695 435 Office: +44 (0) 207 608 6951 -----------------------------------------------------