How to get better alignment results of PAcBio data?

beyg · 05-23-2019, 05:23 AM

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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05-23-2019, 05:23 AM	#1
beyg Junior Member Location: Islamabad Join Date: May 2019 Posts: 1	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.