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a2iEditing / RNAEditingIndexer

A tool for the calculation of RNA-editing index for RNA seq data
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Clarification on error messages #37

Closed hengjwj closed 2 years ago

hengjwj commented 2 years ago

Hi, I wanted to check what the following error means:

[2022-03-15 07:16:03,167] A2IEditingIndex ERROR Failed Processing of L_stage22_rep1! Traceback (most recent call last): File "Tools/EditingIndex/A2IEditingIndex.py", line 793, in load_and_process_sample File "Tools/EditingIndex/A2IEditingIndex.py", line 922, in get_stranded_strands_and_counts File "Tools/EditingIndex/A2IEditingIndex.py", line 964, in get_refseq_majority ZeroDivisionError: integer division or modulo by zero

I received a bunch of these for a particular region I'm investigating and in the output summary file, only three samples showed up even though the cmpileup was generated for all my samples. Is it safe to say the AEI and/or coverage is too low to detect in these samples?

Thank you!

shalomhillelroth commented 2 years ago

Hi,

That's definitely seems the case. If you wish to double-check you can try to extract the coverage for those regions using samtools.

Best,

Shalom Hillel Roth