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ygidtu / trackplot

trackplot is a tool for visualizing various next-generation sequencing (NGS) data, including DNA-seq, RNA-seq, single-cell RNA-seq and full-length sequencing datasets.
https://trackplot.readthedocs.io/
BSD 3-Clause "New" or "Revised" License
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By increasing the event length #93

Closed sivasubramanics closed 1 year ago

sivasubramanics commented 1 year ago

Hello Team, Thanks for the great tool. I was trying to plot a region of 1 MB and the code crashes showing "KeyError: 'exon_id'", that doesn't make any sense. Because just by reducing the event length the plot completes with no issues.

Do we have maximum limit for event length?

CMD works: trackplot -e Dovetail_reconstructed_14OCT2019_v4_lg_2:51486277-51490011:+ -r pangenome.gtf --density density.list --output LK057.pdf -d 600 CMD didn't work: trackplot -e Dovetail_reconstructed_14OCT2019_v4_lg_2:50486277-51490011:+ -r pangenome.gtf --density density.list --output LK057.pdf -d 600

- Siva

ygidtu commented 1 year ago

Hi, It seems like this error caused by your gtf file missing some of exon_id tags. Could you please give me more information like which version of trackplot do you use, and an exmaple of your gtf file for us to debugging?

Yours Best

sivasubramanics commented 1 year ago

It was due to the absent tag "exon_id" in the GTF file. I converted gff2gtf using agat tools, and the output GTF is of GTF3.0 format, which by default does not come with "exon_id" tag. I had to edit the GTF file, then it worked.

Probably we mention in the help that the GTF annotation should be of specific version?

ygidtu commented 1 year ago

Hi Siva, Thanks for your feedback, I'll check the GTF format generated by agat, and try to fix this in next release. Yours, Best