De novo Assembly and Annotation
The raw paired end reads were trimmed and quality controlled by SeqPrep
(https://github.com/jstjohn/SeqPrep ) and Sickle
(https://github.com/najoshi/sickle ) with default parameters.
Then clean data from the samples
(skin and brain) were used to do de novo assembly with Trinity
(http://trinityrnaseq.sourceforge.net/)(Grabherr et al., 2011). All the
assembled transcripts were searched against the NCBI protein
nonredundant (NR), String, and KEGG databases using BLASTX to identify
the proteins that had the highest sequence similarity with the given
transcripts to retrieve their function annotations and a typical cut-off
E-values less than 1.0×10−5 was set. BLAST2GO
(http://www. blast2go.com/ b2ghome)(Conesa et al., 2005) program was
used to get GO annotations of unique assembled transcripts for
describing biological processes, molecular functions and cellular
components. Metabolic pathway analysis was performed using the Kyoto
Encyclopedia of Genes and Genomes (KEGG,
http://www.genome.jp/kegg/)(Goto, 2000).