Sentence examples for using the trinity pipeline from inspiring English sources

For de novo transcriptome analysis, processed RNA-seq reads were assembled using the Trinity pipeline (Haas et al. 2013).

The filtered RNA-Seq data were used for de novo transcriptome assembly using the Trinity pipeline with default parameters.

A single representative de novo assembly was generated from a concatenation of the four libraries using the Trinity pipeline (r2014_07 17) [ 5, 6].

The eight RNA-seq samples were used to perform a de novo transcriptome assembly using the Trinity pipeline (Grabherr et al. 2011; Haas et al. 2013).

Gene expression levels were determined using the Trinity pipeline; utilizing BWA read mapping (Li and Durbin 2009) and RSEM read count normalization (Li and Dewey 2011).

The raw assembly of the C. capitata transcriptome was constructed using the Trinity assembly pipeline with all filtered reads from all eighteen libraries pooled into one dataset.

The clean reads of the three libraries were de novo assembled using the Trinity Program (V 2.2.0) with default parameters (Grabherr et al. 2011).

Reads were then assembled using the Trinity suite (r20131110) [ 121], and then re-mapped to the assembly using the RSEM (v1.2.13) pipeline, with bowtie2 as the mapper [ 122, 123].

The transcriptome sequences were assembled using the Trinity program.

Lactate secretion was determined using the Trinity Lactate Kit (Trinity Biotech, Jamestown, NY, USA) according to the manufacturer's protocol.

The nine Illumina RNASeq data sets were assembled with Trinity [ 28] 2012-01-25p1 using trinitynity.pl wrapper and options '--bflyHeapSpace 15G' and '--no_meryl'.