Inverted BigWig and ASE

[Lijingtangbo]

Hi, thank you for creating figeno and making it public. It is very useful for me. I would like to ask you some suggestions.

• Could you let me know if it is possible to plot inverted BigWig track for some applications i.e. sense/antisense RNA-seq?
• What type of track should I use to plot allelic specific expression information i.e. informative SNP allelic bias?

Thanks!

[e-sollier]

Hi,

Thanks for the suggestion to allow inverted bigwig tracks. It was not possible, but I've just added a new version 1.0.8 for figeno, where I added an option to have the bigwig and coverage tracks upside down. You can install the new version with pip install figeno==1.0.8 and then include "upside_down":true in the config file, for the track that you want to be upside down.

Concerning allele-specific expression, what kind of figures do you want exactly ? Figeno currently has an undocument "ase" track type, which can generate this kind of figure: It shows the variant allele frequencies of heterozygous SNPs in DNA and RNA, and shows where on the chromosomes these SNPs lie. Is this the kind of figure that what you want ?

For now, this feature is undocumented because it requires inputs which are quite unusual:

• a VCF of SNPs from the DNA (optional, only if you want to show the VAF in the DNA)
• a table of allelic read counts in the RNA (only at positions where there are heterozygous SNPs in the DNA), generated with ASEReadCounter

I have the following nextflow workflow to generate these files: https://github.com/CompEpigen/wf_WGS (with run_ase: true), but this only supports human data. Here is the config file used to generate the figure above, together with the input files: config_ase.json inputs.zip

If you think this track type could be useful, I could add it to the documentation, but considering that the inputs are difficult to produce I don't think many users would be interested in it. Or if you have suggestions for alternative ASE plots, feel free to share them.

[Lijingtangbo]

Thank for your kind reply! I will definitely try "upside down" option. Actually, I realised that you already had an ase track. I tried but with a little changes.

• error in ase.py line 70. df_ase["altCount_DNA"] = refCount_DNA to df_ase["altCount_DNA"] = altCount_DNA
• little change in track_ase.py'. the box is too wide in my plot, so I change frombar_width=(box["right"]-box["left"]) 0.7 / len(VAFs)tobar_width=(box["right"]-box["left"]) 0.01 / len(VAFs)`

[Lijingtangbo]

Hi, I think in this version 1.0.8. The default setting for BigWig plot is"upside_down":true.

[e-sollier]

Oups, thanks for noticing this! I've fixed this is 1.0.9. I've also corrected the df_ase["altCount_DNA"] = refCount_DNA in ase.py and for the ase track, I added a "bar_width" option, which is by default at 0.7 but which you can set to 0.01 if you want to get narrower bars like you did in your figures.

[Lijingtangbo]

Thank you very much!

[Lijingtangbo]

I think 1.0.9 has a little problem. see attached.

[e-sollier]

I think this should be fixed with 1.0.10, did you try it ?