Alignment and mapping methodology impact transcript abundance estimation

SRR109.txt -> list of accession numbers used for experimental analysis. simulatedquants -> Bowtie2 pipeline quantification results on the 109 samples, that are used to simulate datasets for futher analysis. scriptsSimulate -> scripts to generate simulated data using the 109 quantification results on real data. The "runme.sh" file can be executed to generate a "data" folder with all the simulated reads and ground truth count and TPM values. table1Data -> fasta and true abundance files for 10 replicates of simulated data (from human transcriptome GENCODE v29) used to generate table 1 of the manuscript. table2Data -> fasta and true abundance files for 10 replicates of simulated data (from mouse transcriptome PWK variant) used to generate table 2 of the manuscript. HSVquants -> quantification results from all methods on the 3 HSV-1 infected datasets used for differential expression testing. Note that the text files in every dataset folder contain adjusted p-values from DESeq2 for each method. refFastas -> the human and mouse reference fasta files containing the decoy sequences, which can be used to construct the salmon index.