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guigolab / ggsashimi

Command-line tool for the visualization of splicing events across multiple samples
MIT License
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No reads in the specified Area error #38

Closed padwalmk closed 4 years ago

padwalmk commented 4 years ago

Hi, I am using the ggsashmi to plot some of the transcripts from gtf file, However when I see in the IGV there are reads for exons as well as junctions. However, when I run sashami-plot script I get error "No reads in the specified area." Example jpeg for the transcripts from IGV.

I am running following command for the plotting. sashimi-plot.py -b bam_list -C 4 -L 3 -c chr22:39696699-39700075 -o MSTRG10006 -g ../Final_novel.gtf
Screenshot from 2020-06-30 10-25-20

emi80 commented 4 years ago

Hi @padwalmk, apologies for the late reply.

Could you please check that the chromosome name in the bam corresponds with the one you passed via command line (I cannot see the chromosome name in the IGV screenshot)? If everything looks fine, could you please send us a small example to reproduce the issue?

padwalmk commented 4 years ago

Hi, Thank you for the reply, Actually I was using ggshashami script for plotting novel lncRNA from bam files. These lncRNAs are not expressed et al in some of the samples so, when script encounter such samples it throw error and take exit.

I have changed the code and remove the exit(1) from code and now I am getting plot. However, I now encounter new problem, I have given colour details for three group, but I am getting color plot for only one group. I am attaching a sample file produced after changing code. This is example file, where nodal-metastasis should have blue and primary should have green colour but I am getting only Gray colour in two groups.

MSTRG20120 1

padwalmk commented 4 years ago

Thank you, I have tried you updated script, and it throw another eroor ...

"Traceback (most recent call last): File "/usr/local/bin/sashimi-plot.py", line 671, in R_script += make_R_lists(id_list, bam_dict[strand], overlay_dict, args.aggr, intersected_introns) File "/usr/local/bin/sashimi-plot.py", line 491, in make_R_lists x, y, dons, accs, yd, ya, counts = d[k] KeyError: u'SRR5553891'"

But when I removed continue from line in which you have added, it run smoothly. But the colour for group is still not coming. Another thing When I try to overlay with same code, it draw colour but the not as specified by color setting.

Thank you for quick response.

emi80 commented 4 years ago

I can have a look at this. But having a small example to reproduce the problem would really help to debug it.

Thanks.

emi80 commented 4 years ago

The new HEAD on dev should fix this. Please let me know if it works.

If it is fine, I would move the color problem to another GitHub issue.

Thanks a lot.

padwalmk commented 4 years ago

Hi, Thank you, work perfectly.

MSTRG20120 1

The new HEAD on dev should fix this. Please let me know if it works.

If it is fine, I would move the color problem to another GitHub issue.

Thanks a lot.