All the pacbio reads can be downloaded from SRP093919
Note:Analysis of PacBio single-molecule long-reads. Bamboo genome sequences and annotated gene models were downloaded from NCGR (Peng et al., 2013). ConsensusTools from the smrtanalysis_2.3.0 (Pacific Biosciences of California, Inc) was used from the command line to get reads of insert. Then, the command-line wrapper script pbtranscript.py from the smrtanalysis_2.3.0 was used for the full-length read identification. Both 5' and 3' Clontech kit primers seen as well as a poly(A) tail signal preceding the 3' primer were used to produce strand-specific full-length reads (https://github.com/PacificBiosciences/cDNA_primer/wiki/RS_IsoSeq-(v2.3)-Tutorial-%231.-Getting-full-length-reads). Then SMRT long reads from Pacific BioSciences were corrected by Illumina reads using LSC 1.alpha with Bowtie 2 version 2.2.1 alignment (Au et al., 2012).