I am using bwa-mem in my local galaxy to map paired-end sequencing reads to a bacterial reference genome.
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 ran bwa mem using the reference genome generated by the BWA INDEX tool, using the following bwa-mem parameters - I selected paired-end reads, set SAM/BAM specifications (all auto) and used simple illumina mode
Is there an additional step I need to do in order to visualize the mapped reads?
When I visualize the bwa-mem output (bam) file using Integrated Genome Browser (IGB), I only see reads mapping to about 3Kb when the reference genome is around 6.2Mb. When I open the bwa-mem output on IGV it gives me the following errors:
Warning: unsuccessful attempt to execute ‘Range byte’ request to host localhost
Could not locate genome with ID: pseuAeru
Error loading http://localhost:8080/display_application/2a56795cad3c7db3/igv_bam/local_default/d8524d8a26e52f97/data/galaxy_2a56795cad3c7db3.bam: An error occurred while accessing: http://localhost:8080/display_application/2a56795cad3c7db3/igv_bam/local_default/d8524d8a26e52f97/data/galaxy_2a56795cad3c7db3.bam Error loading BAM file: java.io.EOFException
I appreciate any help