Hi to everyone,
I have rna seq data (bacterial) grown in rich and poor growth mediums. we have carried out 2 replicates of each of these conditions.
my question is, how do we computationally estimate how similar our biological replicate data is? what files will I use to determine the variability between two replicates? will I have to use the bam files (post alignment to a reference) or raw fastq files to ascertain this? is there a program that will take reads/alignments from the 2 replicates and tell me the percentage similarity between the two datasets?
I know this sounds simple, and I went through quite a few threads, but could not understand how to work this out. I am struggling.
would really appreciate any input.
Thank you,
N
I have rna seq data (bacterial) grown in rich and poor growth mediums. we have carried out 2 replicates of each of these conditions.
my question is, how do we computationally estimate how similar our biological replicate data is? what files will I use to determine the variability between two replicates? will I have to use the bam files (post alignment to a reference) or raw fastq files to ascertain this? is there a program that will take reads/alignments from the 2 replicates and tell me the percentage similarity between the two datasets?
I know this sounds simple, and I went through quite a few threads, but could not understand how to work this out. I am struggling.
would really appreciate any input.
Thank you,
N
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