2015
DOI: 10.1093/nar/gkv1013
|View full text |Cite
|
Sign up to set email alerts
|

NCLscan: accurate identification of non-co-linear transcripts (fusion,trans-splicing and circular RNA) with a good balance between sensitivity and precision

Abstract: Analysis of RNA-seq data often detects numerous ‘non-co-linear’ (NCL) transcripts, which comprised sequence segments that are topologically inconsistent with their corresponding DNA sequences in the reference genome. However, detection of NCL transcripts involves two major challenges: removal of false positives arising from alignment artifacts and discrimination between different types of NCL transcripts (trans-spliced, circular or fusion transcripts). Here, we developed a new NCL-transcript-detecting method (… Show more

Help me understand this report

Search citation statements

Order By: Relevance

Paper Sections

Select...
2
1
1
1

Citation Types

5
92
0

Year Published

2016
2016
2024
2024

Publication Types

Select...
6
1
1

Relationship

0
8

Authors

Journals

citations
Cited by 109 publications
(97 citation statements)
references
References 101 publications
5
92
0
Order By: Relevance
“…Current circRNA detection methods are incapable of distinguishing linear NCLs from circular NCLs (i.e., circRNAs) [15, 27] since they may share the same back-splicing junction [28]. In this study, the false positive rate caused by the linear intragenic chimeric transcripts was estimated as following: We identified 4,164 NCLs from the circRNA-enriched (poly(A) - /ribo - ) transcriptome using the tool NCLscan [15]. These NCLs were all circRNAs theoretically since the linear transcripts have been digested by RNase R during the library preparation.…”
Section: Resultsmentioning
confidence: 99%
See 2 more Smart Citations
“…Current circRNA detection methods are incapable of distinguishing linear NCLs from circular NCLs (i.e., circRNAs) [15, 27] since they may share the same back-splicing junction [28]. In this study, the false positive rate caused by the linear intragenic chimeric transcripts was estimated as following: We identified 4,164 NCLs from the circRNA-enriched (poly(A) - /ribo - ) transcriptome using the tool NCLscan [15]. These NCLs were all circRNAs theoretically since the linear transcripts have been digested by RNase R during the library preparation.…”
Section: Resultsmentioning
confidence: 99%
“…In the same way, we identified 1,711 NCLs in the parallel total RNA transcriptome, which may consist of both linear NCLs and circRNAs. Of them, 686 were mutual to both transcriptomes, they were potential circRNAs [15]. Worthy of mention, three experiment-validated circRNAs (CDYL, GSE1, and ZNF609) were in the mutual list.…”
Section: Resultsmentioning
confidence: 99%
See 1 more Smart Citation
“…A stringent detection approach requires the use of a tool with high precision and therefore a controlled amount of false‐positives. NCLScan is a good example. This approach ensures a small list of strong candidates by stringent filtering and by imposing high detection thresholds.…”
Section: Rna‐seqmentioning
confidence: 99%
“…Simulated RNA-Seq data (paired end reads, 100 ;bp and 6000 backsplicing reads for each sample) were generated by randomly choosing 200 chiastic transcripts based upon the Arabidopsis thaliana and rice genome annotations, respectively (Supplementary Data). The sensitivity, precision and sensitivity ;+ ;precision (a comprehensive value) (Chuang et al , 2016) was used to evaluate the performance of the three methods. The results indicate that PcircRNA_finder has a higher sensitivity (74–88%) than either find_circ or CIRCexplorer (each about 20%) and better precision (63–67%) compared to find_circ and CIRCexplorer, (72 and 100%, respectively) in the two test genomes (Supplementary Data).…”
Section: Benchmarkmentioning
confidence: 99%