Mutations in RNA-Seq Data

[AsoBioInfo]

Hi there,

I am somewhat new to RNA-Seq so my questions will be a bit naive!

• I had run Bowtie for the alignment purposes and will be using Samtools for variations. Just need a clarification, that .bam files will be containing the Variation data aligned with the reference genome... Right?
  
  
• One more quick question, what are the reference files for any sample files (which have the extension of .gbk or .fasta). What's the purpose of those reference files? I have searched a lot for these files but I am unable to have a clear concept about these files....

I have already used the DEseq, DEGseq and edgeR for plotting and graphs of RNA seq data but I want to find the mutations in RNA seq data and this can be done using these tools (like Samtools for variants)

Thanks!