Detecting mutations from RNAseq data

[chudar]

HI,

I have RNAseq data from samples which has to be aligned to reference Transcriptome. Later I would like to compute number of times a particular nucleotide in reference transcript has been mutated to another nucleotide. For an instance number of times nucleotide "A" in reference transcript is mutated to "C" in treated_transcript.

So far I used RNAseq for quantifying gene expression and finding the differential gene expression.

Any guidance would be highly appreciated.

Thanks in advance.

[GenoMax]

https://www.biostars.org/p/102836/

[chudar]

https://www.biostars.org/p/102836/

Hi GenoMax,

Thank you very much for guidance. I went through it but the pipeline has been designed to find the genomic variants. The organism on which I work doesnt has Genome yet and at present only transcriptome is available. So is there any other alternate way to find the point mutation from RNAseq data for every sample. Thanks in advance.