Are all those .sam mandatory ?

[jkreplak]

Hi, I was doing some tests using finder for a large plant genome. At the end of alignments steps, a .sortedByCoord.out.sam and a _for_psiclass.sam are created and removed only at the end of the whole pipeline. I'm using 24 RNA-seq library in this test, and only the alignments dir is around 2.5 To. Most of it is due to those .sam. Would it be possible to suppress (or best not generate them..) them at the end of the alignment ? Are they really used in some other steps ? Thanks, Jonathan