Running Griffin on TSS

[Irfanwustl]

Hi, Thanks for the great tool. While I was able to run Griffin on TFBS using your demo, I am wondering how we can run it in TSS. In the TFBS case, for every TF Griffin needs a dedicated file of many binding sites for that particular TF. However, for TSS, every gene has only one TSS. So, how should we provide the TSS info? A demo will be very helpful.

Thanks

[adoebley]

Hi,

Thanks for the question!

You can provide the TSS info in a single TSV file and then make a few changes to the config to analyze sites individually:

chrom_column: position_column: strand_column: chroms:

CNA_normalization: True #normalizes the coverage around each TSS to 1 so you can compare samples with different copy numbers for a given TSS (norm_window is +/- 5000 bp by default) individual: True #save the coverage at each TSS separately exclude_outliers: False #when looking at individual sites, you don't need to exclude outlier positions within sites

I added an example config in the development branch: https://github.com/adoebley/Griffin/blob/development/snakemakes/griffin_nucleosome_profiling/config/config_TSS.yaml

To make sure your reverse TSS are getting flipped properly, look for a line like this in the log and check that there are 0 undirected sites: Total sites (fw/rv/undirected/total): 18112/17805/0/35917

Let me know if you have any more questions or this isn't working for you!

-Anna-Lisa

[Irfanwustl]

Many thanks. However, it seems the example config file link you provided does not exist. Can you please have a look?

-Irfan

[adoebley]

Hi Irfan,

Sorry about that. I fixed the link above. Let me know if it's still not working.

-Anna-Lisa