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Hey did you ever figure out a solution to this problem? I'm having the same one...Leave a comment:
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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!
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