Hi,
I am using IsoTools 2.0 to detect and analyze alternative splicing events, and I am having difficulty extracting the actual genomic coordinates of the affected exon(s) for each AS event.
For downstream analysis, I would like to obtain the coordinates of the event itself, for example:
exon skipping: coordinates of the skipped exon
alternative 5'/3' splice site: coordinates of the affected alternative region or exon boundary
intron retention: coordinates of the retained intron
mutually exclusive exons: coordinates of the alternative exons
Currently, the AS event output provides information such as the transcripts involved and splice junction coordinates, but it is not straightforward to recover the exact exon coordinates directly from the event table. In particular, for exon skipping events, the output appears to describe the flanking splice junctions rather than directly reporting the skipped exon coordinates.
It would be very useful if IsoTools could optionally include event-level genomic coordinates in the AS event output, for example columns such as:
event_chrom
event_start
event_end
event_strand
event_exon_start
event_exon_end
event_region_type
or, for events involving multiple regions/exons, a structured field such as:
event_regions = [(chrom, start, end, strand, region_type), ...]
This would make it much easier to connect IsoTools AS events with downstream analyses such as genome annotation, motif analysis, overlap with regulatory regions, visualization, or comparison with other AS tools.
A minimal example is exon skipping: given the transcripts in which the exon is included and the transcripts in which it is skipped, it should be possible to report the coordinates of the exon that differs between the two transcript sets. However, doing this manually from the current output requires reconstructing transcript exon structures and handling strand, transcript IDs, and edge cases.
Would it be possible to add an option to output explicit event-region coordinates for each AS event?
Thanks for developing and maintaining IsoTools.
Hi,
I am using IsoTools 2.0 to detect and analyze alternative splicing events, and I am having difficulty extracting the actual genomic coordinates of the affected exon(s) for each AS event.
For downstream analysis, I would like to obtain the coordinates of the event itself, for example:
exon skipping: coordinates of the skipped exon
alternative 5'/3' splice site: coordinates of the affected alternative region or exon boundary
intron retention: coordinates of the retained intron
mutually exclusive exons: coordinates of the alternative exons
Currently, the AS event output provides information such as the transcripts involved and splice junction coordinates, but it is not straightforward to recover the exact exon coordinates directly from the event table. In particular, for exon skipping events, the output appears to describe the flanking splice junctions rather than directly reporting the skipped exon coordinates.
It would be very useful if IsoTools could optionally include event-level genomic coordinates in the AS event output, for example columns such as:
event_chrom
event_start
event_end
event_strand
event_exon_start
event_exon_end
event_region_type
or, for events involving multiple regions/exons, a structured field such as:
event_regions = [(chrom, start, end, strand, region_type), ...]
This would make it much easier to connect IsoTools AS events with downstream analyses such as genome annotation, motif analysis, overlap with regulatory regions, visualization, or comparison with other AS tools.
A minimal example is exon skipping: given the transcripts in which the exon is included and the transcripts in which it is skipped, it should be possible to report the coordinates of the exon that differs between the two transcript sets. However, doing this manually from the current output requires reconstructing transcript exon structures and handling strand, transcript IDs, and edge cases.
Would it be possible to add an option to output explicit event-region coordinates for each AS event?
Thanks for developing and maintaining IsoTools.