Alignment and mapping methodology impact transcript abundance estimation

<pre>SRR109.txt -&gt; list of accession numbers used for experimental analysis. simulatedquants -&gt; Bowtie2 pipeline quantification results on the 109 samples, that are used to simulate datasets for futher analysis. scriptsSimulate -&gt; scripts to generate simulated data using the 109 quantification results on real data. The &quot;runme.sh&quot; file can be executed to generate a &quot;data&quot; folder with all the simulated reads and ground truth count and TPM values. table1Data -&gt; 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 -&gt; fasta and true abundance files for 10 replicates of simulated data (from mouse transcriptome PWK variant) used to generate table 2 of the manuscript. refFastas -&gt; the human and mouse reference fasta files containing the sequence-similar decoy sequences, which can be used to construct the salmon index for SA.</pre>