User: rlorigro

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rlorigro10
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Posts by rlorigro

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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 ...
written 21 days ago by rlorigro10
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Pysam read reference positions and sequence do not match
... 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 ...
samtools pysam pileup tview written 3.3 years ago by rlorigro10 • updated 3.2 years ago by Biostar ♦♦ 20

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Popular Question 3.2 years ago, created a question with more than 1,000 views. For Pysam read reference positions and sequence do not match

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