Limits...
Global and unbiased detection of splice junctions from RNA-seq data.

Ameur A, Wetterbom A, Feuk L, Gyllensten U - Genome Biol. (2010)

Bottom Line: We have developed a new strategy for de novo prediction of splice junctions in short-read RNA-seq data, suitable for detection of novel splicing events and chimeric transcripts.When tested on mouse RNA-seq data, >31,000 splice events were predicted, of which 88% bridged between two regions separated by <or=100 kb, and 74% connected two exons of the same RefSeq gene.Our method also reports genomic rearrangements such as insertions and deletions.

View Article: PubMed Central - HTML - PubMed

Affiliation: Department of Genetics and Pathology, Rudbeck laboratory, Uppsala University, Uppsala, Sweden. adam.ameur@genpat.uu.se

ABSTRACT
We have developed a new strategy for de novo prediction of splice junctions in short-read RNA-seq data, suitable for detection of novel splicing events and chimeric transcripts. When tested on mouse RNA-seq data, >31,000 splice events were predicted, of which 88% bridged between two regions separated by

Show MeSH
SplitSeek results viewed in the UCSC genome browser. (a) Predicted splice junctions in the gene Fpgs. (b) The two grey boxes give a schematic view of how deletions and insertions are detected. The genome browser image below shows the SplitSeek results in the last exon and 3' UTR of the Nol10 gene on chromosome 12. Three events are predicted, a splice junction (to the left), a deletion (in the middle,) and an insertion (to the right). The predicted insertion and deletion are both supported by the mRNA AK148210, as indicated by the orange arrows at the bottom.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
getmorefigures.php?uid=PMC2864574&req=5

Figure 4: SplitSeek results viewed in the UCSC genome browser. (a) Predicted splice junctions in the gene Fpgs. (b) The two grey boxes give a schematic view of how deletions and insertions are detected. The genome browser image below shows the SplitSeek results in the last exon and 3' UTR of the Nol10 gene on chromosome 12. Three events are predicted, a splice junction (to the left), a deletion (in the middle,) and an insertion (to the right). The predicted insertion and deletion are both supported by the mRNA AK148210, as indicated by the orange arrows at the bottom.

Mentions: As seen in Figure 3, an almost a linear correlation exists between the number of SplitSeek predictions and the total number of reads in the three samples. This demonstrates that we have not yet reached saturation and would detect many more splice junctions by deeper sequencing, as indicated by extrapolated dotted lines in Figure 3. The SplitSeek results can be viewed in the UCSC genome browser [14], as illustrated by two example regions in Figure 4. The first example shows a gene with many predicted exon-exon boundaries, including alternative splicing (Figure 4a), whereas the second demonstrates the possibility of detecting insertions/deletions in the sample (Figure 4b). In both cases, the SplitSeek predictions agree with annotated splice junctions, insertions, and deletions almost at nucleotide resolution. The reason that the position is not always exact is that the first few nucleotides in an intron may coincide with the first bases of the next exon, thereby resulting in a slight overextension of the anchor during the alignment procedure.


Global and unbiased detection of splice junctions from RNA-seq data.

Ameur A, Wetterbom A, Feuk L, Gyllensten U - Genome Biol. (2010)

SplitSeek results viewed in the UCSC genome browser. (a) Predicted splice junctions in the gene Fpgs. (b) The two grey boxes give a schematic view of how deletions and insertions are detected. The genome browser image below shows the SplitSeek results in the last exon and 3' UTR of the Nol10 gene on chromosome 12. Three events are predicted, a splice junction (to the left), a deletion (in the middle,) and an insertion (to the right). The predicted insertion and deletion are both supported by the mRNA AK148210, as indicated by the orange arrows at the bottom.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC2864574&req=5

Figure 4: SplitSeek results viewed in the UCSC genome browser. (a) Predicted splice junctions in the gene Fpgs. (b) The two grey boxes give a schematic view of how deletions and insertions are detected. The genome browser image below shows the SplitSeek results in the last exon and 3' UTR of the Nol10 gene on chromosome 12. Three events are predicted, a splice junction (to the left), a deletion (in the middle,) and an insertion (to the right). The predicted insertion and deletion are both supported by the mRNA AK148210, as indicated by the orange arrows at the bottom.
Mentions: As seen in Figure 3, an almost a linear correlation exists between the number of SplitSeek predictions and the total number of reads in the three samples. This demonstrates that we have not yet reached saturation and would detect many more splice junctions by deeper sequencing, as indicated by extrapolated dotted lines in Figure 3. The SplitSeek results can be viewed in the UCSC genome browser [14], as illustrated by two example regions in Figure 4. The first example shows a gene with many predicted exon-exon boundaries, including alternative splicing (Figure 4a), whereas the second demonstrates the possibility of detecting insertions/deletions in the sample (Figure 4b). In both cases, the SplitSeek predictions agree with annotated splice junctions, insertions, and deletions almost at nucleotide resolution. The reason that the position is not always exact is that the first few nucleotides in an intron may coincide with the first bases of the next exon, thereby resulting in a slight overextension of the anchor during the alignment procedure.

Bottom Line: We have developed a new strategy for de novo prediction of splice junctions in short-read RNA-seq data, suitable for detection of novel splicing events and chimeric transcripts.When tested on mouse RNA-seq data, >31,000 splice events were predicted, of which 88% bridged between two regions separated by <or=100 kb, and 74% connected two exons of the same RefSeq gene.Our method also reports genomic rearrangements such as insertions and deletions.

View Article: PubMed Central - HTML - PubMed

Affiliation: Department of Genetics and Pathology, Rudbeck laboratory, Uppsala University, Uppsala, Sweden. adam.ameur@genpat.uu.se

ABSTRACT
We have developed a new strategy for de novo prediction of splice junctions in short-read RNA-seq data, suitable for detection of novel splicing events and chimeric transcripts. When tested on mouse RNA-seq data, >31,000 splice events were predicted, of which 88% bridged between two regions separated by

Show MeSH