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-   -   How to get better alignment results of PAcBio data? (http://seqanswers.com/forums/showthread.php?t=89499)

beyg 05-23-2019 05:23 AM

How to get better alignment results of PAcBio data?
 
HI. I am trying to align PAcBio data (data from third generation sequencer) using bwa mem. I am getting very less number of aligned reads in SAM file having coverage of less than 10X. I tried to use minimap2 as well for alignment but again the quality of SAMfile isn,t good. I am getting only few unique reads and they are aligning on reference with soft clipping. Moreover, my SAM file contains many cases of multimapping. The average read length of spots is >3kb.
What other options are available to get better alignment results? I am working with this data for the very first time.


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