REditools2 (HPC-reditools) de-novo editing prediction from RNAseq?
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Entering edit mode
19 months ago
RNAseqer ▴ 230

I am having some trouble with REditools2 (HPC-Reditools). In the original version of reditools there was a python script for de-novo prediction of editing sites from RNAseq data using a strategy outlined in Picardi et al 2012. I assumed reditools2 would have this same feature. However, after inputting the appropriate files (bam alignments from our RNAseq data) the output seems to be giving me more than predicted editing sites, it seems to be giving a table with all nucleotides with any coverage, and every base that was found there:

Region  Position    Reference   Strand  Coverage-q30    MeanQ   BaseCount[A,C,G,T]  AllSubs Frequency   gCoverage-q30   gMeanQ  gBaseCount[A,C,G,T] gAllSubs    gFrequency
chr1    15210   C   2   1   40.00   [0, 0, 1, 0]    CG  1.00    -   -   -   -   -
chr1    15211   T   2   1   40.00   [0, 0, 0, 1]    -   0.00    -   -   -   -   -
chr1    15212   G   2   1   40.00   [0, 1, 0, 0]    GC  1.00    -   -   -   -   -
chr1    15213   T   2   1   40.00   [0, 0, 0, 1]    -   0.00    -   -   -   -   -
chr1    15214   T   2   1   40.00   [0, 1, 0, 0]    TC  1.00    -   -   -   -   -
chr1    15215   T   2   1   40.00   [0, 1, 0, 0]    TC  1.00    -   -   -   -   -
chr1    15216   G   2   1   40.00   [0, 1, 0, 0]    GC  1.00    -   -   -   -   -
chr1    15217   A   2   1   40.00   [0, 1, 0, 0]    AC  1.00    -   -   -   -   -


Is there a way to limit the output to predicted editing sites only? Or is there a function that uses this table as input to do prediction? If so it is not clear to me from reading the github how to do that. Any assistance would be appreciated!

editing reditools2 prediction RNAseq • 534 views