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  • Tools or ways to find out variants in RNA seq data ?????

    I know that we can find out variants in DNA seq data using different tools(GATK, Samtools..........) but I wonder if there are any tools to find out variants in RNA seq data.

    I understand the concept of RNA editing and also the ongoing debate behind it.
    Please can anyone help me with how to go with this approach further ?
    Also, please suggest me tools to find out variants in RNA seq data

  • #2
    I believe that you can use GATK and samtools on RNA-Seq data.

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    • #3
      I've run both GATK and samtools mpileup on RNA-Seq data, and I got better results with samtools. GATK is more geared towards genome SNPs, and I'm sure by playing around with the settings I could get better results with variant calling for RNA reads, but I haven't tried that yet.

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      • #4
        Thanks.............!!!!!!!!!! I guess this might help
        I will try both GATK and samtools.

        Here a found a list to analyse seq data..........



        I thought this might help as well.....!!!!!!!!!!!

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