Table 2.

Example datasets and accessory scripts for ShortStack analysis. These resources along with a complete tutorial are available at [12].

Datasets/scripts	Description
Athaliana_167.fa	FASTA file containing unmasked reference nuclear and organelle genomes for Arabidopsis thaliana (TAIR 10). The genomes were downloaded from www.phytozome.net and sequence headers were shortened.
Athaliana_167.inv	einverted generated file containing inverted repeats identified in Athaliana_167.fa.
SRR051927_even.fastq	Untrimmed small RNA-seq dataset from above ground tissues of Arabidopsis, in FASTQ format. From NCBI SRA SRR051927. Only the even- numbered reads.
SRR051927_odd.fastq	Untrimmed small RNA-seq dataset from above ground tissues of Arabidopsis, in FASTQ format. From NCBI SRA SRR051927. Only the odd-numbered reads.
ath_hp_mb19_SStack_Athal_167.txt	Coordinates of miRBase 19 Arabidopsis thaliana MIRNA hairpins relative to the TAIR10 genome.
invert_it.pl	Perl script for faster processing of einverted predicted inverted repeats
ShortStack_TUTORIAL.pdf	Detailed tutorial instructions