I am using bwa-mem in my local galaxy to map paired-end sequencing reads to a bacterial reference genome. I just want to be sure I didn’t make a mistake with the analysis before asking whether this was a problem with sequencing - as fastq on the files looked good.
I used DMs to reference the genome using the following steps:
Create DBKey and reference genome - used existing dbkey (found my species), using accession number from NCBI for the fasta sequence of my reference genome, left ‘sort by chromosome name: as is’.
Then I created indexes using SAM FASTA index builder, Picard index builder, TwoBitbuilder and BWA-MEM index building (in this order).
Then I visualized the bwa-mem output (bam) file using Integrated Genome Browser (IGB). The reference genome is around 6.2Mb. When I open the bam alignment file on IGB, the reads only map to about 3Kb (the ‘load data’ button does not load new sequence data past this point).