- Any existing output files will be overwritten after execution.
- Always use
--peek-guessto remove spurious barcode hits.
Run on CLR subread data:
$ lima <movie>.subreads.bam <barcodes>.fasta <demux>.bam $ lima <movie>.subreadset.xml <barcodes>.barcodeset.xml <demux>.subreadset.xml
Run on CCS / HiFi data:
$ lima <movie>.ccs.bam <barcodes>.fasta <demux>.bam $ lima <movie>.consensusreadset.xml <barcodes>.barcodeset.xml <demux>.consensusreadset.xml
If you do not need to import the demultiplexed data into SMRT Link, it is advised to use
--no-pbi, omit the pbi index file, to minimize time to result.
CLR: --same CCS: --same --ccs
CLR: --different CCS: --different --ccs
$ lima m54317_180718_075644.subreadset.xml Sequel_RSII_384_barcodes_v1.barcodeset.xml \ m54317_180718_075644.demux.subreadset.xml --different --peek-guess
Lima processes input reads grouped by ZMW, except if
--per-read is chosen. All barcode regions along the read are processed individually. The final per-ZMW result is a summary over all barcode regions, a pair of selected barcodes from the provided set of candidate barcodes; subreads from the same ZMW will have the same barcode and barcode quality. For a particular target barcode region, every barcode sequence gets aligned as given and as reverse-complement, and higher scoring orientation is chosen; the result is a list of scores over all candidate barcodes.
If only same barcode pairs are of interest, symmetric/tailed, please use
--same to filter out different barcode pairs.
If only different barcode pairs are of interest, asymmetric, please use
--different to require at least two barcodes to be read and remove pairs with the same barcode.