<![CDATA[BOL: How to get better alignment results of PAcBio data?]]> https://bioinformaticsonline.com/answers/view/39385/how-to-get-better-alignment-results-of-pacbio-data? https://bioinformaticsonline.com/answers/view/39385/how-to-get-better-alignment-results-of-pacbio-data Wed, 22 May 2019 02:01:07 -0500 https://bioinformaticsonline.com/answers/view/39385/how-to-get-better-alignment-results-of-pacbio-data <![CDATA[How to get better alignment results of PAcBio data?]]> HI! I am Nadia.

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 sam file 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 read length of spots is >2kb.

What other options are available to get better alignment results? I am working with this data for the very first time.

]]> Nadia Baig