sample_status_file_creator.py

[sixingchen718]

Hi, Thank you develop this cool tool. I've completed running REDItoolDnaRna.py on my RNA-seq results, and I want to proceed with differential analysis. However, I'm stuck. Some protocols suggest creating a sample information file and then running the get_DE_events.py program. I tried this but wasn't successful. Others mention using sample_status_file_creator.py to generate the required sample information file (.sif), but I haven't seen this script mentioned in your guidance. Could you please guide me through the correct process? Thank you very much. Best, Sixing

[gianfilippo]

Hi, same issue here. How did you solve it ? Thanks

[yr542]

@gianfilippo Did you resolve your issue with the sif file. I have been have a lot of issues with get_DE_events.py and I figured out how the sample informations file should look but I cannot seem to get the get_DE_events.py so much so I have had to convert to python3 and then am still debugging (whether in python 2 or 3 it seems to have quite a few issues. If you haven't figured out the sample informations file format (SIF) it seems that CTRL or DIS are required in a Status column and the sample names in the Sample column. The scaffold of what I used is below:

Sample,Status
SRRExperimental-01,DIS
SRRExperimental-02,DIS
SRRExperimental-03,DIS
SRRControl-01,CTRL
SRRControl,CTRL
SRRControl,CTRL

Note(s):

• Each sample name must start with SRR according to what I see in the code.
• The files must be organized as SampleNameFolderAsInSampleColumn/editing/outTable_*.
• You must use DIS for the experimental samples and you must use CTRL for the control samples.

The notes are just what I have observed however, I just cannot seem to get the get_DE_events.py to work.

[gianfilippo]

Hi, no, sorry. Still stuck

[yr542]

I have been working on/editing the get_DE_events script as it seems to have quite a few requirements and might have a couple of bugs.

Requirements Seem To Be:

• Your samples must be in a sample folder with SRR front of it under a subfolder called editing with outTable_ where `` is a random number

Scaffold:

SRRsampleName/editing/outTable_12345678

• You must add chr if it is not already present in the data.
• You should remove mitochondrial region rows
• You should remove all K* contig rows

This is all I have so far but I do not know if it helps @gianfilippo as sadly I still cannot seem to get it to work.

[gianfilippo]

thanks!!! I will give it a try as soon as I go back to this project. Will keep you posted.