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The expression count data, cluster mapping, and annotated results.
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Unigenes with BLAST results were mapped and annotated using the mapping and annotation functions of B2GO.
However, mapping and annotating this information will need to be coordinated.
We developed the BridgeDb app for Cytoscape to provide utilities for mapping and annotating identifiers in the network context.
After mapping and annotating the tags, the data were normalized by equalizing the total number of tags for all samples in MMSDK and DGE, respectively.
Blast2go [ 27] was used for blasting, mapping, and annotating the contigs by comparing the assembled sequences to the non-redundant protein (nr) data base of the National Centre for Biotechnology Information (NCBI) (Table 2).
To assign gene ontology terms to each annotated sequence, successful blast hits were mapped and annotated using Blast2GO for the entire assembled transcriptome with the annotation cut-off threshold set to 55 and the GO level weighting set to 5. The single lane of Illumina HiSeq2000 produced close to 128 million paired-end reads (2 × 101 bp).
Integration sites from published datasets [3], [19] were re-mapped and annotated according to the same criteria.
Sequence reads were mapped and annotated using Bowtie2 software [ 43].
Read statistics for the sequencing data when mapped and annotated to the sheep genome.
In total, 360,000 sequence reads were obtained, assembled to 12,200 contigs, functionally mapped, and annotated.
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