multiple sample differential RNA editing/SNP after novoalignment

[12jrowley2]

Any programs out there that will take multiple aligned RNA-seq datasets from treatment and control samples with biological replicates and compare them for differences in single base pair substitutions/indels?

RNA-seq samples are sequenced with Illumina paired end sequencing and aligned using novocraft novoaligner.

It seems I should be able to do this without realignment, and independent of additional comparisons genomic sequences, by determining which base pairs are consistently different between the treatment and control samples. Any ideas will be helpful.

Thanks!

[Boel]

Dont think that there are any programs out there developed for that exact task. I'm using samtools pileup as a starting point in a similar analysis, but there is a lot of downstream stuff to take care about. Would be interested if there is a publicly avaliable program to do this as well.

[Garima Singh]

hello every one,i'm working on novoaligner.do anyone have any idea about how much time novoaligner will take for alignment..