I would like to map hundreds of fastq.gz single-end RADseq files to a single reference genome.
But, bwa mem is making a map file (.sam) for every fastq file. So I end up with hundreds of individual maps. I want a single map with all fastq files mapped to the reference.
I have tried hundreds of failed commands, here is one failed example:
bwa mem -t 16 ../reference.Arrow.fasta ../fastqs/*.F.fq.gz > RADs_mapped.sam
Any ideas what I am doing wrong? Or what is wrong with my expectation of a single .sam file with all sequences mapped to my reference?
But, bwa mem is making a map file (.sam) for every fastq file. So I end up with hundreds of individual maps. I want a single map with all fastq files mapped to the reference.
I have tried hundreds of failed commands, here is one failed example:
bwa mem -t 16 ../reference.Arrow.fasta ../fastqs/*.F.fq.gz > RADs_mapped.sam
Any ideas what I am doing wrong? Or what is wrong with my expectation of a single .sam file with all sequences mapped to my reference?
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