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  • swapnil2188
    replied
    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.....!!!!!!!!!!!

    Leave a comment:


  • pbluescript
    replied
    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.

    Leave a comment:


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

    Leave a comment:


  • 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

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