De novo recontruction of barley transcription factors from CI16151 to preserve SNPs and indels

The nucleotide sequence of 25 barley genes were reconstructed from RNA-Seq data collected from a infection time-course experiment from a single cultivar (CI16151). Raw reads, from a total of 18 CI16151 samples, were mapped to the barley genome using a STAR with the alignIntronMin and alignIntronMax set to 20 and 10,000 respectively. The genomic locus for each of the 25 genes were extracted from the V2 version of Barley Morex annotation [citation reqd.]. Aligned CI16151 raw reads were then subset for only those extracted loci and converted into a fastq file. Trinity was used to assemble the reawreads de novo to preserve the SNPs and indels. Out of 25 genes, 11 genes were found to contain at least one SNP.