The correct identification of differentially expressed genes (DEGs) between specific conditions is a key in the understanding phenotypic variation. High-throughput transcriptome sequencing (RNA-Seq) has become the main option for these studies. Thus, the number of methods and softwares for differential expression analysis from RNA-Seq data also increased rapidly. However, there is no consensus about the most appropriate pipeline or protocol for identifying differentially expressed genes from RNA-Seq data. This work presents an extended review on the topic that includes the evaluation of six methods of mapping reads, including pseudo-alignment and quasi-mapping and nine methods of differential expression analysis from RNA-Seq data. The adopted methods were evaluated based on real RNA-Seq data, using qRT-PCR data as reference (gold-standard). As part of the results, we developed a software that performs all the analysis presented in this work, which is freely available at https://github.com/costasilvati/consexpression. The results indicated that mapping methods have minimal impact on the final DEGs analysis, considering that adopted data have an annotated reference genome. Regarding the adopted experimental model, the DEGs identification methods that have more consistent results were the limma+voom, NOIseq and DESeq2. Additionally, the consensus among five DEGs identification methods guarantees a list of DEGs with great accuracy, indicating that the combination of different methods can produce more suitable results. The consensus option is also included for use in the available software.

Aims. Cosmogenic isotopes provide the only quantitative proxy for analyzing the long-term solar variability over a centennial timescale. While essential progress has been achieved in both measurements and modeling of the cosmogenic proxy, uncertainties still remain in the determination of the geomagnetic dipole moment evolution. Here we aim at improving the reconstruction of solar activity over the past nine millennia using a multi-proxy approach. Methods. We used records of the 14 C and 10 Be cosmogenic isotopes, current numerical models of the isotope production and transport in Earth's atmosphere, and available geomagnetic field reconstructions, including a new reconstruction relying on an updated archeo-and paleointensity database. The obtained series were analyzed using the singular spectrum analysis (SSA) method to study the millennial-scale trends. Results. A new reconstruction of the geomagnetic dipole field moment, referred to as GMAG.9k, is built for the last nine millennia. New reconstructions of solar activity covering the last nine millennia, quantified in terms of sunspot numbers, are presented and analyzed. A conservative list of grand minima and maxima is also provided. Conclusions. The primary components of the reconstructed solar activity, as determined using the SSA method, are different for the series that are based on 14 C and 10 Be. This shows that these primary components can only be ascribed to long-term changes in the terrestrial system and not to the Sun. These components have therefore been removed from the reconstructed series. In contrast, the secondary SSA components of the reconstructed solar activity are found to be dominated by a common ≈2400-year quasi-periodicity, the so-called Hallstatt cycle, in both the 14 C and 10 Be based series. This Hallstatt cycle thus appears to be related to solar activity. Finally, we show that the grand minima and maxima occurred intermittently over the studied period, with clustering near lows and highs of the Hallstatt cycle, respectively.