General FAQ

BAM tags explained

Following BAM tags are being used:

  • ib Barcode summary: triplets delimited by semicolons, each triplet contains two barcode indices and the read counts, delimited by comma. Example: 0,1,20;0,3,5
  • ic Number of reads used to generate consensus. If less than is, this means that reads were down-sampled when consensus-calling
  • im Read names associated with this isoform
  • is Number of reads associated with this isoform
  • it List of barcodes/UMIs clipped during tag
  • iz Maximum number of subreads used for polishing
  • rq Predicted accuracy for polished isoform
  • XA Order of tag names
  • XC Cell/group barcode sequence tag
  • CB Cell/group barcode sequence tag. This is an alias for XC, but its presence indicates that the barcode has been corrected
  • CR Raw cell/group barcode sequence tag
  • XG PacBio’s GGG UMI suffix tag
  • XM UMI sequence tag
  • XO Overhang sequence tag
  • nb Edit distance between corrected cell/group barcode and raw cell/group barcode
  • gp Pass/fail for cell/group barcode correction using a truth-set. 1 for pass, 0 for fail
  • nc Number of known cell/group barcodes in the truth-set sharing the shortest distance from the raw barcode. If this number is > 1, this indicates ambiguity in remapping
  • oc Original known cell/group barcodes in the truth-set sharing the shortest distance from the raw barcode

Quality values are capped at 93.

The binary does not work on my linux system!

Binaries require SSE4.1 CPU support; CPUs after 2008 (Penryn) include it.

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