How to tackle low reads in RNA-Seq data and compute differential expression

Question

[Dataminer]

Hi,

Our department has some old RNA-Seq data that means low reads as well.

We have 3 replicates for a sample. FPKM and TPM was computed on these samples using RSEM and alignment was done using STAR in RSEM setup.

The reads are in the range of 3.2 to 3.8 million. This single end RNA-Seq experiment was done in 2011 and I would expect more read counts. But that is not the case.

The low number of read counts is becoming an issue while computing DEG across different conditions using edgeR.

My question how can I use this data set efficiently with this low read count and what tools shall I use. Presently I am using edgeR and looking for DEG at FDR 0.05.

Kindly give your comments.

Thank you

[rpolicastro]

What organism is this for?