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Hi All
I use BWA to map Solid reads (Genomic) to reference. Normaly I used -q parameter to trim low quality end of reads (This significantly improve mapped read %).
I have two problems, are they bugs in BWA.
1. BWA dosent do soft triming of Solid reads it allways dose hard trim.
2. for Unmapped reads it trims only reads but dosent trim quality value. Which results in error (sequence and quality missmatch) when I use samtools or Picard for post processing.
I extensively use BWA for Illumina reads and it never gave these problems. It only occure when I use BWA for Solid reads.
Dose any one get same problem and if yes whats the solution.
I use BWA to map Solid reads (Genomic) to reference. Normaly I used -q parameter to trim low quality end of reads (This significantly improve mapped read %).
I have two problems, are they bugs in BWA.
1. BWA dosent do soft triming of Solid reads it allways dose hard trim.
2. for Unmapped reads it trims only reads but dosent trim quality value. Which results in error (sequence and quality missmatch) when I use samtools or Picard for post processing.
I extensively use BWA for Illumina reads and it never gave these problems. It only occure when I use BWA for Solid reads.
Dose any one get same problem and if yes whats the solution.
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