Dear all, I have sequences of small RNAs which were produced using the GAII, I have my counts table and I need to test which sequences have different expression between treatments. I have started to use DEseq package. But I would like to know if it correct to use the Deseq package which is fro RNAseq or if there is a package for small RNA sequences. Thanks for your help. Andreia -- -------------------------------------------- Andreia J. Amaral Unidade de Imunologia Clínica Instituto de Medicina Molecular Universidade de Lisboa email: andreiaamaral@fm.ul.pt andreia.fonseca@gmail.com [[alternative HTML version deleted]]

Hi Andreia On Thu, 15 Apr 2010 13:50:19 +0100, Andreia Fonseca wrote: > I have sequences of small RNAs which were produced using the GAII, > I have my counts table and I need to test which sequences have different > expression between treatments. I have started to use DEseq package. But I > would like to know if it correct to use the Deseq package which is fro > RNAseq or if there is a package for small RNA sequences. DESeq does not make any assumption about the type of data, except for that they are counts. So, using it for small RNA-Seq is perfectly fine. The step before, i.e., making the count table, is what depends on the assay type. For small RNA, you may have more problems with ambiguous matches, sequencing into adapters, etc., but it seems that you have already dealt with this. Cheers Simon