Read alignment rates to the genome varied between three libraries; for the rich and nutrient limited samples, 90%% or 89%% of reads aligned respectively; for the MI-late sample only 23%% of reads aligned.
Given that the two libraries when assembled separately gave rise to a total of 11,885 assembled sequences, we can estimate that approximately 2,271 sequences were shared between the two libraries, for an overlap of about 19%.
Sampling statistics accounts for most of the differences between libraries in that read count differences between technical replicates of the same library, or between libraries derived from the same biological sample, scaled as √N irrespective of the read count N. The variation in read counts between two libraries was always smaller than 5√N for a given read count.
A web tool IDEG6 was used for detection of differentially expressed genes between two libraries using Fisher exact test [ 91].
Eight libraries for channel catfish and four libraries for blue catfish were produced.
Each of these genes had at least one hit between the two libraries, except for the MADS domain, which had no hits in either library (Table 3).
Looking at their length profiles, we found the mean read length to be slightly different between the two libraries, 38 nt for L. donovani and 46 nt for L. braziliensis, however, the median read length was similar (33 nt and 34 nt, respectively).
Two methods were used to define DEGs: DEGseq software based on p value estimates and 2-fold RPKM differences between the two libraries as a threshold for each gene.
From the raw data, we saw correlations of 0.8966 between the two libraries from G699N and 0.7836 for the two libraries from G761T.
Thus, this overlap of small RNA coverage between the two libraries allowed us to look for genes, which might be regulated strain specifically on the basis of small RNA abundance.
