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Reaction plates were thermocycled, and endpoint reads were conducted on the ABI 7900HT sequence detection system.
Mapping and processing of mRNA-seq reads were conducted using TopHat software [ 40].
Alignment of the SAM file and removal of duplicated reads were conducted using Picard (http://picard.sourceforge.net) and SAMtools [ 31].
When reads were conducted blindly by a panel of independent experts, the overall sensitivity was 88.7% (86.8%too 90.4%) and specificity was 91.2%89.0%to to 93.0%).
De novo assemblies of genomic and transcriptomic reads were conducted in CLC Genomics Workbench (CLC bio, Aarhus, Denmark) using standard parameters.
First, reference assemblies of channel catfish expressed short reads and blue catfish expressed short reads were conducted separately using all existing catfish ESTs as a reference.
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Sorting of sequence reads based on index sequences and the subsequent extraction of sequence tags from reads was conducted using a script written in Perl.
Quality control of reads was conducted using FastQC (Andrews 2010).
Assembly of the expressed short reads was conducted in several ways.
Illumina sequencing, with 100-bp paired-end reads, was conducted on a HiSeq 2000 (Illumina).
Bioinformatic analysis of trimmed RNA-seq reads was conducted using the Tuxedo Suite [ 68].
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