My case is:
We have a deep-sequencing for RNA: two samples (WT and mutation) and 3 replicates for each one.
These small RNA sequences were map to ref-genome.
The ref-genome was seperated into 500bp windows along the whole genome.
We wanna identify the windows with decreased express from WT to Mutation.
Firstly, I try to use two different methods to estimate the size factors.
1. I try to use total counts of reads to estimate the size factors.
p_adj < 0.05 53,866 windows were got.
2. I try to use the estimateSizeFactors to estimate the size factors.
p_adj < 0.05 4,555 windows were got.
Secondly, since the genome is long, I make a filter: the windows with total raw counts in all 6 libraries < 50 were discarded.
1. I try to use total counts of reads to estimate the size factors.
p_adj < 0.05 48,005 windows were got.
2. I try to use the estimateSizeFactors to estimate the size factors.
p_adj < 0.05 464 windows were got.
I donot know I should use the total counts or use estimateSizeFactors to estimate the size factors.
We have a deep-sequencing for RNA: two samples (WT and mutation) and 3 replicates for each one.
These small RNA sequences were map to ref-genome.
The ref-genome was seperated into 500bp windows along the whole genome.
We wanna identify the windows with decreased express from WT to Mutation.
Firstly, I try to use two different methods to estimate the size factors.
1. I try to use total counts of reads to estimate the size factors.
p_adj < 0.05 53,866 windows were got.
2. I try to use the estimateSizeFactors to estimate the size factors.
p_adj < 0.05 4,555 windows were got.
Secondly, since the genome is long, I make a filter: the windows with total raw counts in all 6 libraries < 50 were discarded.
1. I try to use total counts of reads to estimate the size factors.
p_adj < 0.05 48,005 windows were got.
2. I try to use the estimateSizeFactors to estimate the size factors.
p_adj < 0.05 464 windows were got.
I donot know I should use the total counts or use estimateSizeFactors to estimate the size factors.
Comment