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a2iEditing / RNAEditingIndexer

A tool for the calculation of RNA-editing index for RNA seq data
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About source code of AEI #36

Open yangdingyangding opened 2 years ago

yangdingyangding commented 2 years ago

Hi,

We'd like to compute the AEI on some samples with a modified pipeline of RNA editing identification, so we need to skip the variant calling step and compute the AEI directly based on the resulting VCF files. The RNAEditingIndexer can only accept BAM as inputs, so we want to go into the source file and start from the point where all variant sites have been called.

However, we cannot find the source file for RNAEditingIndexer in this repository. Could you please help with this? Thanks.

shalomhillelroth commented 2 years ago

Hi,

The RNAEditingIndexer does no variant calling. It calculates the editing level of predefined regions for each inputted BAM file. If you wish to calculate the level from you sites simply convert your VCF to BED and use that as the regions input.

Is that what you need?

yangdingyangding commented 2 years ago

Hi,

Yes, that is exactly what we'd like to do. I just found that option on the commandline help output (it is not available in the README). I'll try if this works. Thanks!