title: RNA-seq of Brachypodium distachyon : flag and second leaves four days after anthesis
design: Single end (50 bp) bar-coded cDNA libraries were prepared for multiplex sequencing using the TruSeq RNA sample preparation kit ver.2. Barcode removal and filtering of low quality reads were executed using the command line tools cutadapt (-e 0.1, -O 5, -m 15) and FASTX-Toolkit (fastq_quality_trimmer: -l 35, -t 28, fastq_quality_filter: -q 20, -p 90), respectively. Sample sequences were aligned to the Brachypodium reference genome (Bd21-3 v.1) using the Bowtie2 aligner within TopHat2 (-i 20 -I 10000).