I have two data sets of NGS RNA Seq. I have a computer (Linux based with all the programmes of Galaxy) but with 16 GB RAM. When I start computing the de novo assembly, the computer does it for few hours only and then shows that at least 20 days remaining. How much RAM is needed to do de novo assembly?
Dear Xie I have maize uninoculated and inoculated with Colletotrichum graminicola RNA Seq Data (RAW data). In order to know the differentially expressing genes I have to assemble the data and look for the genes differentially expressing. I also want to know secretome of fungus putative in planta.
Padder, as Xie told you, you don't need to make the de-novo assembly of your RNA-seq data. As you have a reference genome, use it to align the reads. From there you can count the reads aligned to each feature/contig/gene and then perform the statistical analysis to address whether or not the reads are more abundant in the inocilated vs inoculated samples.
Now, for the secretome... i guess that can't be answered by RNA-seq, right?
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