NGS-Trex: Next Generation Sequencing Transcriptome profile explorer

BMC Bioinformatics

Table 1 Benchmark.

Label given in Carraro et al.	Carraro et al.	NGS-Trex	Corresponding label in NGS-Trex
Total reads	802214	802214	Total reads (1, 2)
Processed reads	731628	796352	Processed reads (2)
Partly aligning to Human Genome	80570	84593	Mapped low similarity (2)
Completely aligning to Human Genome	651058	691530	Mapped reads (1, 2)
Mapped at one genome position	614434	563190	Mapped with low frequency (2)
Mapped against Known Gene DB	597565	539492	Genic (2)
Mapped against RefSeq	476337	466524	Classified as "T" (2)
Represented mRNAs	17887	20500	Identified transcripts (2)
Represented genes	11366	13415	Identified genes (1, 2)

Summary of the comparison between the results shown by Carraro et al. [8] and the results obtained from NGS-Trex analysis. Data shown in the table are available from the summary table of the project in NGS-Trex website (1) or in the statistical report linked to the dataset (2). Differences can be mainly explained by different programs used, annotation releases and sources (UCSC genome browser data were used by Carraro, while NGS-Trex mainly relies on annotation data available from NCBI).

ISSN: 1471-2105