For these 143 99%% confident AEI signal SNPs, the mean (median) raw reads of reference and variant alleles are 120 (105) and 75 (31) respectively, while the mean (median) read ratio is around 3.36 (3.36).
The mean raw and cleaned read lengths were 286 and 290 bp, respectively.
miRNAs with a mean less than 2 raw read counts across all samples were removed.
In contrast, DESeq and edgeR estimate the means and variances of raw read counts under a negative binomial distribution and use exact tests to identify differentially expressed transcripts.
In contrast, DESeq, edgeR and EBSeq estimate the means and variances of raw read counts under a negative binomial distribution and use exact tests to identify differentially expressed transcripts.
Deep sequencing of the small RNA libraries generated the mean number of raw reads, 10,372,041 and 9,105,582, for PS1 and PS4, respectively (Table 1).
For cross-sample comparisons, we normalized raw read counts for these samples using the TMM method (trimmed-mean of M values; a weighted trimmed mean of the log expression ratios [ 53]) as implemented in the edgeR package [ 54] (http://www.bioconductor.org).
The raw read count comparison was done similarly by first normalized to a mean read of 10,000, then log2 transformed and compared to the expected values.
The raw read counts generated by featureCounts [ 16] were normalized by TMM (trimmed mean of M-values) in edgeR first, followed by standard differential analysis.
