[cc'ing galaxy-user as this may be useful information to other users.] Hi Zovoilis, I was mistaken in writing that Galaxy cannot sort SAM files. Galaxy can sort SAM files; here is an example history that illustrates the sorting of a SAM file: http://test.g2.bx.psu.edu/u/jeremy.goecks/h/sorting-sam-file-for-cufflinks There are two steps in sorting a SAM file: (1) removing SAM headers via the 'remove lines from beginning of a file' tool and (2) using the 'sort data in ascending or descending order' tool to sort by chromosome name and then by position. Samtools provides a single-step process for sorting SAM files, and we expect to add this capability to Galaxy in the future so that the above 2-step process can be replaced by this single step. Best, J.