Arctic char log read counts

• Main Author: Prokkola, Jenni
• Format: Dataset
• Language: unknown
• Published: figshare 2017
• Subjects: 60806 Animal Physiological Ecology; FOS Biological sciences; 60408 Genomics; Arctic; Davidson
• Online Access: https://dx.doi.org/10.6084/m9.figshare.5662489.v1; https://figshare.com/articles/Arctic_char_log_read_counts/5662489/1

Read counts from RNA-sequencing experiment in Arctic char (Prokkola et al.). Rows correspond to genes and columns correspond to samples. Reads can be downloaded from NCBI SRA (accession SRP068854). The used reference is available at DDBJ/EMBL/GenBank under the accession GEKT00000000. The trimmed PE reads from all samples were aligned against the assembly using Bowtie2, ignoring discordant and mixed alignments and allowing a maximum of 40 multiple alignments per read. Read counts per cluster were obtained using Corset (Davidson and Oshlack 2014). Clusters that were expressed with >1 counts per million reads (cpm) in at least 3 samples across all 18 samples were included in the analysis. Data were normalized for library sizes in Studio using edgeR package TMM-normalization (Robinson and Oshlack 2010) and normalized log counts of reads per million mapped reads in each sample exported.