Meaning of the output files of daric normalize, and link with daric runhmm

[mzytnicki]

Hello,

I successfully run daric normalize, and I would like to run daric runhmm.

However, I do not know which files I should use for the -f, --deltaPIS parameter.

Namely, daric normalize produced several files, and I guess I should use one, or two of them.

Would it be possible to provide the list of commands that you used in your article?

The files that daric normalize produced are:

• cond1-vs-cond2_cond1_avg_PIS.bedGraph
• cond1-vs-cond2_cond2_avg_PIS_before-norm.bedGraph
• cond1-vs-cond2_deltaPIS.before-norm.bedGraph
• cond1-vs-cond2_deltaPIS.bedGraph
• cond1-vs-cond2_cond2_avg_PIS_after-norm.bedGraph
• cond1-vs-cond2.txt
• cond1-vs-cond2_background_distribution_for_delta-PIS.png
• cond1-vs-cond2_p-value.bedGraph

Moreover, I do not know the meaning of these files.
Would it possible to give a short description?

Last, the file cond1-vs-cond2_p-value.bedGraph, which should contain p-values in the 4-th column, has values greater than 1, which is unexpected for p-values.
Are they p-values, or maybe -log of p-values?

Thanks again.

[ykai16]

Great to know that you have successfully run daric normalize. For 'runhmm', please use 'cond1-vs-cond2_deltaPIS.bedGraph' for the '--deltaPIS' parameter.

p-value in the 'cond1-vs-cond2_p-value.bedGraph' file is the -log10P-value.

Will add a description for those files soon in the documentation. Thanks!

[mzytnicki]

Dear @ykai16
I wish you all the best for 2024.
I tried to start runhmm with the file you suggested, yet, I had another error:

File "[...]/hmmlearn/base.py", line 799, in _accumulate_sufficient_statistics_log
    stats['start'] += posteriors[0]
IndexError: index 0 is out of bounds for axis 0 with size 0

I could not understand why the posteriors have not been set. I could share the file if you need.

Thanks again!

[ykai16]

Hi @mzytnicki , could you share the full error message you got and the files you used for running ruhmm?

[mzytnicki]

Sure, thanks!
You can find the files here: https://filesender.renater.fr/?s=download&token=7450d74a-23eb-4d17-81a6-1df43993edb5
(they will be available 2 weeks).
You have the bedgraph, and the error output file.

The command was:

daric runhmm -n es_vs_npc -f es-vs-npc_deltaPIS.bedGraph --reso 100000 --species mm10 --outdir results

[ykai16]

Hi, just fixed the issue and pushed a new version v0.2.20 to pypi. Please uninstall daric and install it again using pip with the command "pip install daric". Let me know if there are still problems around.

[mzytnicki]

Works like a charm, thanks!