As some transcripts have very long introns before they are spliced, using the genome coordinate system will make the visualization less informative if someone only focuses on exon regions. See the MCM9 example below:
So, I would like to transform genome coordinates to transcript coordinates. This is another example for MYC transcript (ENST00000621592.5)
The bed12 format for ENST00000621592.5 in the genome coordinate system:
Before I said that it works, there are some issues need to be solved:
1) The tick labels in the top of the plot are not correct (correct labels: 0, 0.5, 1, 1.5, 2kb ?). It is also related to #50.
2) The UTR and CDS regions are not properly plotted. It should be related to the parsing of thick start and end fields in the bed12 format. In the above example, the thick start is 525, and thick end is 1890.
If the two issues are solved, I can add more various tracks based on the transcript coordinate system. I think this visualization will be useful if someone did the transcript-based research.
Hi,
As some transcripts have very long introns before they are spliced, using the genome coordinate system will make the visualization less informative if someone only focuses on exon regions. See the MCM9 example below:
So, I would like to transform genome coordinates to transcript coordinates. This is another example for MYC transcript (ENST00000621592.5)
The bed12 format for ENST00000621592.5 in the genome coordinate system:
The command line for the following plot:
The bed12 format for ENST00000621592.5 in the transcript coordinate system:
The command line for the following plot:
Before I said that it works, there are some issues need to be solved: 1) The tick labels in the top of the plot are not correct (correct labels: 0, 0.5, 1, 1.5, 2kb ?). It is also related to #50. 2) The UTR and CDS regions are not properly plotted. It should be related to the parsing of thick start and end fields in the bed12 format. In the above example, the thick start is
525, and thick end is1890.If the two issues are solved, I can add more various tracks based on the transcript coordinate system. I think this visualization will be useful if someone did the transcript-based research.