Hello, I am trying to map metagenomic Illumina reads to the reference genomes. I used Galaxy LASTZ tool to align Illumina reads to bacteriophage B3, that genomic sequence I downloaded from NCBI website. LASTZ produced an output file in SAM format, the file size is 1.8 MB and contain 16,000 lines. Then, I used Galaxy SAM tools to converted SAM to BAM, and now I am trying to visualize the BAM file in e.g. BamView or Integrated Genome Browser, but without any success. Can anybody tell me what I am doing wrong or how to visualize the alignment, please?
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