Open EMossotto opened 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`
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`