[ensembl-dev] Display BAM with respect to Ensembl features

Thibaut Hourlier th3 at sanger.ac.uk
Thu Aug 22 10:21:11 BST 2013

Hi Ben,
The coordinates of your reads in the bam file should be genomic so there is no easy way. You will need to a write a Perl script to modify your bam file.
As you used Ensembl gene models the transformation of your coordinates should be pretty easy as the reference name in your bam file should be the stable id of your feature. Then you can get the genomic coordinates of the feature with the Perl API and calculate the genomic coordinates of your read.

Hope this help

On 22 Aug 2013, at 01:30, Ben Warren <Ben.Warren at plantandfood.co.nz> wrote:

> Hi,
> I have a RNA-Seq alignment, in the form of a BAM file, where the reads are aligned to gene models, which correspond to the stable ids of gene features in my local Ensembl instance.
> Is there any way to display the BAM in Ensembl? i.e. is it possible to display this BAM which references Ensembl gene features, not the scaffolds or contigs in a Ensembl assembly/coordinate-system?
> Cheers
> Ben
> Ben Warren
> Research Technologist
> F: +64 9 925 7001
> ben.warren at plantandfood.co.nz
> www.plantandfood.co.nz
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