The Ensembl 60 release sees two changes in our data upload capabilities
First off Ensembl can now “attach” a BAM file. BAM is the compressed form SAM – Sequence AlignMent files – which has become the dominant way to package up next-generation sequencing data. A BAM (or SAM file) has both the sequence and the alignment of a set of reads in a compact form (BAM makes it even more compact). Critically you can index a BAM file allowing programs rapid access to particular “Slices” of the reads by genomic position. Alignment tools such as Maq, BWA, SOAP can produce BAM files; a variety of analysis tools are written around BAM files, and now Ensembl can view BAM files.
To make a BAM file viewable you need to have access to a website where you can put files (like you local web space, perhaps an institutional thing). Call MyGreatExperiment.bam. You then need to index the BAM file using one of the tools – samtools is the usual one to do this, making a MyGreatExperiment.bam.bai (BAM index) precisely along side it (The Ensembl code is going to make the assumption that the index is called filename.bai). Then go to “Manage your Data” button on any web page in Ensembl, and go to the “Attach BAM” section. And then browse your RNA-seq, Chip-seq, Exome data to your hearts content!