Journal: Viruses

Article Title: Identification of Known and Novel Recurrent Viral Sequences in Data from Multiple Patients and Multiple Cancers

doi: 10.3390/v8020053

Figure Lengend Snippet: Lowest p -values of clusters established by the pipeline. The p -values are arranged by feature of the strongest significant association of each of the 6165 clusters. The 50 features involved as strongest associations have been coloured by type: biological (red), methodological (green), and technical (blue). The boxes span the first and third quartiles. The dark band inside each box represents the median. The whiskers of the boxes extend to the lowest and highest values within a distance of 1.5 times the interquartile range. As can be seen, most p -values were above 1e-24, but a few methodological features have associated clusters with very low p -values, such as f056, f068, f069, f076, f079, and f084. The library preparation kit ScriptSeq v2 RNA-Seq, Illumina (f084) displays strongly associated clusters with p -values as low as 3.04e-89 that mapped as species Avian myeloblastosis-associated virus . Clusters that were annotated as NCBI species Parvovirus NIH/CQV were associated to laboratory-kit RNeasy MinElute, Qiagen (f076) with minimal p -value 5.48e-38. Finally, a cluster annotated as Acanthocystis turfacea chlorella virus MN0810.1 (ATCV) was associated to DNase/RNase: Promega DNase stop solution (f069) with p -value = 4.19e-12.

Article Snippet: In addition, a single cluster annotated as NCBI taxonomy species Acanthocystis turfacea Chlorella virus MN0810.1 (accession JX997174.1, taxa-id 1278272) with lowest associated p -value ( p -value = 4.19e-12) to laboratory kit DNase/RNase: Promega DNase stop solution (f069).

Techniques: RNA Sequencing, Virus

Journal: Viruses

Article Title: Identification of Known and Novel Recurrent Viral Sequences in Data from Multiple Patients and Multiple Cancers

doi: 10.3390/v8020053

Figure Lengend Snippet: Unmapped clusters. The clusters are placed by their strongest associated feature. Feature types are marked in colour as follows: biological (red), methodological (green), and technical (blue). Top: Number of clusters associated to each feature on a log-10 scaled axis. There are 648 associated clusters of feature DNase/RNase: Promega DNase stop solution (f069), and 1 associated cluster to feature Polymerases: Phusion HF, NEB (f086). Bottom: Base-pair length (bp) of all cluster representatives (longest contig of each cluster) on a log-10 scaled axis. The N50 of all unmapped cluster representatives are marked by a brown dot. The longest cluster representative is 33.6 kb with N50 = 617 bp.

Article Snippet: In addition, a single cluster annotated as NCBI taxonomy species Acanthocystis turfacea Chlorella virus MN0810.1 (accession JX997174.1, taxa-id 1278272) with lowest associated p -value ( p -value = 4.19e-12) to laboratory kit DNase/RNase: Promega DNase stop solution (f069).

Techniques: