shimbalama/post_fastGEAR

Blank heatmap?

Closed this issue · 4 comments

Hi,
I'm trying to produce a heatmap from the output of fastGEAR. However the heatmap printed is just a blank plot. The _count and _scatter plots works fine. I do not get any errors when running the script. Any idea on what to check or fix to get it working?

Cheers,
Magnus

HI - not sure sorry. the no error error is always the worst. if you are able to share your data and your cmd line calls I can try replicate it.

Liam

All good! Thanks! I have made a small example, that I've tested and it 'works'.
The command I used: python3 post_fastGEAR.py -i fastgear_results/ -o test_post_fastgear -p ordering.txt.
There is also a .yml file with info on the conda environment I used to run the script.

github_issue_3.zip

I'll try get to this on the weekend

the issue is that neither hutU or group_1996 is in lineage_information.txt. you need to use the SRR ids.