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Converting gaf files to sam/bam?
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Difference between gam and sam/bam files?
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vg convert does not preserve the order of the reads
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Converting gam to gaf
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How to extract high coverage region from BAM?
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Search for reads aligned to multiple chromosomes
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Tutorial: SAM files processing and variants calling in bacterial genomes
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Compare Short Read Alignments To Two References Simultaneously (Based On Reference To Reference Ali…
written by joseph.fass 1<p>I'd love to be able to compare alignments (SAM/BAM; short reads) to two <em>different</em> reference sequences that are aligned to each other. The two (or …
Yes a read can be aligned more than once (I don't specifically know about gam/gaf). It would be called a "multi-mapping" read. You could imagine reads aligning to multiple places because there are multiple copies of a gene (e.g. rRNA) or there can be common domains in multiple genes.