I have generated SHAPE-MaP data with the use of Oxford Nanopore Technology sequencing. As recommended in Shapemapper documentation, I have performed alignment separately and am now trying to run the modular workflow.
I have tried two options that lead to errors when running shapemapper_mutation_parser module.
Option 2:
minimap2 -ax splice --MD --eqx reference.fa sequences.fastq.gz > alignment.sam
shapemapper_mutation_parser -i alignment.sam -o parsed_alignment.mut --input_is_unpaired
Error: MD tag does not match CIGAR string at explicit match operator ('=').
Does anyone have an idea?
Thank you in advance for your help.
Hello,
I have generated SHAPE-MaP data with the use of Oxford Nanopore Technology sequencing. As recommended in Shapemapper documentation, I have performed alignment separately and am now trying to run the modular workflow. I have tried two options that lead to errors when running shapemapper_mutation_parser module.
Option 1: minimap2 -ax splice --MD reference.fa sequences.fastq.gz > alignment.sam shapemapper_mutation_parser -i alignment.sam -o parsed_alignment.mut --input_is_unpaired Error: CIGAR string incorrectly formatted
Option 2: minimap2 -ax splice --MD --eqx reference.fa sequences.fastq.gz > alignment.sam shapemapper_mutation_parser -i alignment.sam -o parsed_alignment.mut --input_is_unpaired Error: MD tag does not match CIGAR string at explicit match operator ('=').
Does anyone have an idea? Thank you in advance for your help.