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a2iEditing / RNAEditingIndexer

A tool for the calculation of RNA-editing index for RNA seq data
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RNAEditing deletes BAMs if executed in the same folder #24

Closed EMossotto closed 3 years ago

EMossotto commented 3 years ago

RNAEditingIndex removes the original BAM file if run in the same folder. I think this should be fixed by refining the clean-up stages.

Here the script to replicate the problem where $BAM is the absolute path to the BAM file.

`DIRE=$(dirname ${BAM}) BB=$(basename ${BAM})

RNAEditingIndex -d $DIRE -f $BB -o . \ --genes_expression /sc/arion/projects/buxbaj01a/enrico/Resources/GenesExpression/MusMusculus/ucscMM10GTExGeneExpression.bed.gz \ --refseq /sc/arion/projects/buxbaj01a/enrico/Resources/RefSeqAnnotations/MusMusculus/ucscMM10RefSeqCurated.bed.gz \ --snps /sc/arion/projects/buxbaj01a/enrico/Resources/SNPs/MusMusculus/ucscMM10CommonGenomicSNPs142.bed.gz \ -gf /sc/arion/projects/buxbaj01a/enrico/Resources/Genomes/MusMusculus/ucscMm10Genome.fa \ -rb /sc/arion/projects/buxbaj01a/enrico/Resources/Regions/MusMusculus/ucscMM10SINE_B1_B2.bed.gz \ --genome UserProvided --paired_end --stranded`