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--ccs typo
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y9c authored and armintoepfer committed May 20, 2019
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4 changes: 2 additions & 2 deletions README.md
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Expand Up @@ -91,7 +91,7 @@ Run on raw subread data:

Run on CCS data:

lima --css movie.ccs.bam barcodes.fasta prefix.bam
lima --ccs movie.ccs.bam barcodes.fasta prefix.bam
lima --ccs movie.consensusreadset.xml barcodes.barcodeset.xml prefix.consensusreadset.xml

If you do not need to import the demultiplexed data into SMRT Link, it is advised
Expand Down Expand Up @@ -967,7 +967,7 @@ The score lead measures how close the best barcode call is to the second best.
Possible solutions without seeing your data:
* Is that sample actually barcoded?
* Are your barcode sequences genetically too close for SMRT sequencing?
Try CCS2 calling first and demultiplex with `--css`.
Try CCS2 calling first and demultiplex with `--ccs`.
* Are the synthesized products clean and not degenerate?
* Did the sequencing run perform optimally, is the accuracy in the expected range?
* Did you run lima twice, first on the original and then on the already
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