plot error

[Tang-pro]

Hi @EricKutschera

python rmats2sashimiplot.py --b1 Y1_5_1.bam,Y1_5_2.bam --b2 Y2_5_1.bam,Y2_5_2.bam -c A03:-:347256:450665:./quant.transcript_models.gff3 --l1 s1 --l2 s2 --exon_s 1 --intron_s 5 -o test5dpa

Is this error due to a different version? Junction reads are almost invisible here。

And another question
-c Whether or not there is a limit on the distance length

My data is ONT DRS

[EricKutschera]

Those warnings about tick labels should not affect the output, but the latest master branch includes a change to avoid the warning: #141

My guess is that the plot shows very few junction reads because they are being filtered out. You have ONT data which likely have insertions and deletions, but rmats2sashimiplot is designed for short-read data where insertions and deletions are less common: #33 (comment)

I don't think there is a limit on the -c coordinate range, but longer regions will take longer to plot

[Tang-pro]

@EricKutschera

Thanks!

Is there any software suitable for long-read RNA-seq (especially ONT DRS) that is capable of drawing sashimi plots?

[EricKutschera]

IGV has a sashimi plot feature:
https://igv.org/doc/desktop/#UserGuide/tracks/alignments/rna_seq/#sashimi-plots

I also tried https://github.com/guigolab/ggsashimi

[Tang-pro]

@EricKutschera

Thank you very much for your reply.

I've tried to draw sashimiplot with IGV before, but the drawing my boss didn't feel satisfied, maybe a little ugly in his opinion. ggsashimi is similar.