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!
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!
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