(a) Single-end reads using the Roche/454 extra-long read Titanium platform generated independently from each pool.
Reference transcriptome was assembled with trimmed reads using Trinity (v2.0.6) (Grabherr et al. 2011; Haas et al. 2013).
Generated mapping data file (SAM file) was processed for filtering out discordant paired reads using in-house Perl scripts.
A quick glimpse of a New York Times article framed and placed on Louise's kitchen countertop reads: "Using Life's Dull Clay to Mold the Fantasy of Life".
Re-alignment of AS reads using IndexDP was done using the same parameters as SMS reads, using the full length of the read.
Clusters of ESTs were further merged based on sister reads using double linkage.
Next the linker sequences were identified and trimmed from individual reads using a customized Perl script.
Unmapped by 454 reads using gsMapper.
We aligned short reads using BWA software.
Adaptor sequences were removed from Illumina reads using cutadapt [ 41].
We simulated bisulfite-converted reads using DNemulator [ 5].
