Coverage on GappedAlignment Pairs
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@lakshmanan-iyer-4597
Last seen 9.6 years ago
Hi Two questions: 1. Is readGapppedAlignmentPairs - the most efficient way to read a paired-end bam file with mulit-mapped reads? I am asking as it takes an enormous amount of time to process and load. 2. How does one work with coverage on GappedAlignmentPairs in the context of RNASeq? The simplest way is to consider each left and right read as separate - essentially loose the "paired" information and calculate coverage. However, if both the left and right pair reads fall within a feature of interest - say an exon, does it imply coverage of the region of the exon between the reads too >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>> LLLLLLLLLL---------------------------RRRRRRRRRR ^^^^^^^^^^^^^^^^^ In the figure above, the exon is represented by ">" and L and R represents the left and right reads aligned to the exon. I am talking about the region represented by "^". Do we assume coverage for this region too? Does Coverage on GappedAlignmentPairs do this? -best -Lax Center for Neuroscience Research Tufts Univeristy School of Medicine Boston, MA [[alternative HTML version deleted]]
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