Output

kallisto_output

Contains the final counts file, kallisto_counts.csv, as well as differential expression results (produced by Sleuth) for all desired comparisons.

edgeR_output

Contains the edgeR differential expression for each comparison, as well as a file with all comparisons combined, combined_edgeR.tsv. The FDRs will not match between the individual and combined files, because the FDR is always calculated at the level of the file. That is, the FDR for combined_edgeR.tsv calculates the FDR across all comparisons jointly.

multiqc_report.html

Standard QC output regarding alignment percentage, numbers of reads, sequence quality, etc.