> 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
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
[cc'ing galaxy-user as this may be useful information to other users.]
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:
There are two steps in sorting a SAM file:
(1) removing SAM headers via the 'remove lines from beginning of a file' tool
(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.