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Showing of 1 reviews. Read groups should have distinct ID values. Only aStart, aEnd were stored, although in that file format they were referred to as rStart, rEnd. Created using Sphinx 1. For example, a duration of frames would round to and then be encoded as codepoint
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The BAM format is a binary, compressed, record-oriented container format for raw or aligned sequence reads. The associated SAM format is a text representation of the same data. In this document we describe the way we make use of the extensibility mechanisms of the BAM specification to encode PacBio-specific information, as well as conventions we adhere to. An example file adhering to this specification will be maintained in the pbcore Python library.
PacBio BAM files adhering to this spec contain the tag pb: The BAM format uses a 0-based coordinate system to refer to positions and intervals on the reference. PacBio also uses a 0-based coordinate system to refer to positions and intervals within sequence reads. A sequence read presented to an aligner is termed a query ; typically this query will be a subsequence of an entire PacBio ZMW read—most commonly, it will be a subread , which is basecalls from a single pass of the insert DNA molecule.
Upon alignment, generally only a subsequence of the query will align to the reference genome, and that subsequence is referred to as the aligned query. Under soft-clipping , the entirety of the query is stored in the aligned BAM, but the CIGAR field indicates that some bases at either end are excluded from the alignment.
Abstractly, we denote the extent of the query in ZMW read as [qStart, qEnd and the extent of the aligned subinterval as [aStart, aEnd The following graphic illustrates these intervals:. In the legacy cmp. Only aStart, aEnd were stored, although in that file format they were referred to as rStart, rEnd.
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