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Posts by rlorigro
Answer: A: convert sam into paf format
... Looks like no one has actually read the question correctly. PAF is missing lots of information compared to SAM, because it is a summary of alignment, but it also has easy access to the alignment start and stop coordinates, sequences lengths, etc. Since PAF is less information-dense you cannot conver ...
... Hi, In order to parse cigar strings and make my own pileup I need to find the reference sequence at the position which each read aligns. However, read.get_reference_positions() seems to be offset from the actual region of alignment, because comparing samtools tview at the first position of alignmen ...
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