Knowing the anchor point the direcon to search for

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Unformatted text preview: air or paired ­end mapping abnormali/es Read ­depth signals Split read alignments 34 Mate ­pair or paired ­end mapping abnormali/es Read ­depth signals Split read alignments 35 Mate ­pair or paired ­end mapping abnormali/es Read ­depth signals Split read alignments 36 Mate ­pair or paired ­end mapping abnormali/es Read ­depth signals Split read alignments Pindel (Ye et al.): detec/on of large dele/ons and medium size inser/ons. •  Some reads may not be mapped because they are just across the break points of deletion events. •  If we can find a proper position to break the read into two fragments and map them separately, we will be able to compute the exact break points and the fragment deleted compared to the reference. 37 General Procedure of Pindel •  All reads are aligned and examined: –  Keep paired ­end reads that only one end can be mapped. The mapped end must be uniquely located in the genome with no mismatch bases while the other end cannot be mapped to anywhere in the genome under a given threshold alignment score. –  For each of those pairs, our Pindel program uses the mapped end to determine the anchor point on the reference genome and the direc/on of the unmapped read. –  Knowing the anchor point, the direc/on to search for the unmapped read and the user defined Maximum Dele/on Size parameter, a sub ­region in the reference genome can be located, where Pindel will break the unmapped read into 2 (dele/on) or 3 (short inser/on) fragments and map the two terminal fragment separately. 38 The “Pa[ern Growth Algorithm” efficiently finds minimum and maximum unique substrings of a given pa[ern against a sequence database 39 Detecting deletion events. Ye K et al. Bioinformatics 2009;25:28...
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This note was uploaded on 02/10/2014 for the course CS 680 taught by Professor Staff during the Fall '08 term at Colorado State.

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