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  • pacBioToCa output reduced reads

    I ran pacBioToCA to correct my pacbio long reads with illumina short reads + pacbio ccs reads. When I started my run, I had:

    illumina short paired-end reads: 1,400,548
    pacbio ccs reads: 3,303
    pacbio long reads: 601,218

    After my run (which did not look like it had any errors), I have only 10,574 error-corrected reads in my output files.

    Why are my reads significantly reduced? Am I doing something wrong?

    Here is my command:
    pacBioToCA -l pacbio.ec -t 16 -s pacbio.spec -fastq pacbio.clr.fastq pacbio.ccs.frg illumina.subset.frg

    Help is much appreciated!

  • #2
    Hey did you ever figure out a solution to this problem? I'm having the same one...

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    • #3
      No, unfortunately I haven't gotten a solution for it :/

      Comment

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