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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..
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..