![]() ![]() You can learn more about our "off-label" use of this format here. Note that there is a variant of BAM that we call uBAM (for unmapped BAM) which holds unmapped read data. Most genomes mappers (including BWA and STAR, our favorite mappers for DNA and RNAseq, respectively) emit SAM or BAM natively. BAMs and CRAMs hold the same information as their SAM equivalent, structured in the same way what is different between them is how the files themselves are encoded. BAM and CRAM are both compressed forms of SAM BAM (for Binary Alignment Map) is a lossless compression while CRAM can range from lossless to lossy depending on how much compression you want to achieve (up to very much indeed). SAM stands for Sequence Alignment Map and is described in the standard specification here. SAM, BAM and CRAM are all different forms of the original SAM format that was defined for holding aligned (or more properly, mapped) high-throughput sequencing data. ![]()
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