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Figure 2 | BMC Genomics

Figure 2

From: Transcriptome sequencing of Atlantic salmon (Salmo salar L.) notochord prior to development of the vertebrae provides clues to regulation of positional fate, chordoblast lineage and mineralisation

Figure 2

Bioinformatics analysis pipeline for RNA-seq. Short reads were checked for quality score and nucleotide distribution, and reads were not trimmed. Reads were mapped to the genome with BWA. Predictions of coding sequences (exon) of the salmon contig assembly were performed using Augustus algorithm. Gene annotations were done by homologous sequence inference against Swissprot, Uniref90 and KEGG databases. Total mapped reads to predicted exons were summarized and normalized using the longest transcript length among all libraries and total number of reads per library. 66569 transcripts/genes were identified in the raw gene list with more than three reads per gene. Differentially expressed gene (DEG) analysis was performed using NOISeq. DEG’s were further clustered by k-mean clustering, KEGG pathway and Gene Ontology ID.

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BMC Genomics

ISSN: 1471-2164

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