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Hello Everyone,
I am new into bioinfo and NGS analysis so I would like if you can help me with ideas to evaluate if two sRNA-Seq experiments are good replicates.
I have the aligment of two sRNA-Seq experiments (the replicates) against the Chromosome 1 of a genome.
I filetered the aligment to exclude structural RNAs. Also, I only selected transcripts of 21 to 24 nt length because I only have interest in the function of this small RNAs.
Using CoverageBed I obtained the coverage depth of every single nucleotide in the Chromosome 1 for both replicates.
In R I checked the correlation using cor.test() with Pearson as method. This gave me a really good score of .98. But then I added 1 to each count of the coverage and applied log scale to both (added 1 to be able to apply log scale, because I had multiple 0 in several position), and the correlation score using the Pearson method dropped to .45.
So I would like to know what do you think. This makes sense or I am totally lost?
Cheers!
I am new into bioinfo and NGS analysis so I would like if you can help me with ideas to evaluate if two sRNA-Seq experiments are good replicates.
I have the aligment of two sRNA-Seq experiments (the replicates) against the Chromosome 1 of a genome.
I filetered the aligment to exclude structural RNAs. Also, I only selected transcripts of 21 to 24 nt length because I only have interest in the function of this small RNAs.
Using CoverageBed I obtained the coverage depth of every single nucleotide in the Chromosome 1 for both replicates.
In R I checked the correlation using cor.test() with Pearson as method. This gave me a really good score of .98. But then I added 1 to each count of the coverage and applied log scale to both (added 1 to be able to apply log scale, because I had multiple 0 in several position), and the correlation score using the Pearson method dropped to .45.
So I would like to know what do you think. This makes sense or I am totally lost?
Cheers!