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  • RNA-seq analysis

    Hi all,

    I am trying to analyze some SOLiD generated RNA-seq data for the first time. Using bwa for the mapping, I have noticed that I am getting between 25-30% of the total reads to map uniquely. This seems like a low number to me but is it what would be expected?

    My second question is in regards to trying to identify SNPs from the transcript reads. For this I have been using samtools. For my samples, 75% of the variants that are identified are indels. I am not sure why there are so many indels and could this be due to a problem with the initial alignment?

    Thank you all for any help and advice..

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