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Error: this SAM file doesn't appear to be correctly sorted!

Could you please add also the function from cufflinks for sorting sam file before use?

Given that you're not using Tophat to map your reads, you'll want to sort your reads before uploading them to Galaxy b/c Galaxy does not (yet?) have a tool to sort SAM files.

[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.