mapping long-reads to a reference library
Hi,
I have long, pacbio, reads and I have a reference library of only repeats, I want to map the long reads on the repeats library using bwa mem, is this command correct?
bwa index mmm.pacbio.fastq.gz
bwa mem mmm.pacbio.fastq.gz repeat-library.fasta | samtools sort -@16 - -o mm.vs.lib.sorted.bam
Do I need reference genome for mapping?
1 answer
You need to index the reference genome, not the fastq files. I think for long reads people prefer minimap2 though these days.
what is the purpose of indexing a genome
Please see the manuals of bwa-mem or minimap2, it explains what to do.
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