given a FASTQ file and a BAM file of aligned reads, is there an efficient way to get all FASTQ reads that are in the original FASTQ but not in the BAM? Perhaps using bedtools. i.e.:
unmapped_script original.fastq aligned.bam > unmapped.fastq
should create an unmapped.fastq file, which is a subset of original.fastq containing only those entries that do not appear in aligned.bam
thank you.