The transcriptome of compatible wheat was assembled by pooling all six RNA-Seq data sets using the Trinity program (Fig. 2a).
The de novo assembly (without a reference) was performed using reads that did not map against the public data set (previously described) using the Trinity assembler [ 68]; contigs of at least 200 bp were allowed, and the parameter "--run_butterfly" was used.
After quality filtering with Condetri (v. 2.0) [ 206] using the default setting, the reads were assembled using the Trinity RNA-seq suite [ 207, 208].
All six RNA-Seq data sets were pooled and assembled using the Trinity program (Fig. 2a).
De novo assembly of RNA-seq data was carried out using the Trinity software package [ 42] with the maximum length expected between fragment pairs set to 300.
The clean reads of the three libraries were de novo assembled using the Trinity Program (V 2.2.0) with default parameters (Grabherr et al. 2011).
The nine Illumina RNASeq data sets were assembled with Trinity [ 28] 2012-01-25p1 using trinitynity.pl wrapper and options '--bflyHeapSpace 15G' and '--no_meryl'.
Using the Trinity method, 52,081,238 high-quality trimmed reads were assembled into a non-redundant set and 108,502 unigenes with an average length of 1,047 bp were generated.
Using the Trinity method, nearly 52,081,238 high-quality trimmed reads were assembled into a non-redundant set of 118,064 unigenes with an average length of 500 bp and an N50 of 599 bp.
Using the Trinity software package (version r2013-02-15 [ 24] 24]) we assembled all the reads together into a final set of 83,967 unique transcripts (isoforms) after filtering for quality of reads and of assembled transcripts [ 22].
Second, we searched for intact open reading frames (ORFs) in these filtered house finch transcripts, using the Trinity tool suite and only transcripts with predicted ORFs longer than 300 bp were kept; we define this set as the unfiltered set.
