I meet a problem when using RNAEditingIndex, the log file told me that program run failed for samtools sort failed to read header from "-", This is my command with the example bam files:
./RNAEditingIndex -d ./TestResources/BAMs/BAMs/ -f _sampled_with_0.1.Aligned.sortedByCoord.out.bam.AluChr1Only.bam -l log -o out -os out --genome hg38
This is the log infomation:
And after checked the log file, I found that bedtools and samtools can run successful when I copy the command and run in in shell:
bedtools intersect -abam ./TestResources/BAMs/BAMs/SRR5962201/SRR5962201_sampled_with_0.1.Aligned.sortedByCoord.out.bam.AluChr1Only.bam -b /media/bora_A/gonglh/2023-08-25-rare-RNA-editing/2023-10-30-GTEx_RNA_editing_level/bin/RNAEditingIndexer/Resources/Regions/HomoSapiens/ucscHg38Alu.bed.gz -split |samtools sort -l 1 -@ 10 -o out/SRR5962201/SRR5962201_region_ucscHg38Alu.bed.gz_alignments.bam -
I meet a problem when using RNAEditingIndex, the log file told me that program run failed for samtools sort failed to read header from "-", This is my command with the example bam files:
./RNAEditingIndex -d ./TestResources/BAMs/BAMs/ -f _sampled_with_0.1.Aligned.sortedByCoord.out.bam.AluChr1Only.bam -l log -o out -os out --genome hg38This is the log infomation:
And after checked the log file, I found that bedtools and samtools can run successful when I copy the command and run in in shell:
bedtools intersect -abam ./TestResources/BAMs/BAMs/SRR5962201/SRR5962201_sampled_with_0.1.Aligned.sortedByCoord.out.bam.AluChr1Only.bam -b /media/bora_A/gonglh/2023-08-25-rare-RNA-editing/2023-10-30-GTEx_RNA_editing_level/bin/RNAEditingIndexer/Resources/Regions/HomoSapiens/ucscHg38Alu.bed.gz -split |samtools sort -l 1 -@ 10 -o out/SRR5962201/SRR5962201_region_ucscHg38Alu.bed.gz_alignments.bam -Looking forward to your replay😊😊