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.


THIS WEBSITE AND CONTENT AND ALL SITE-RELATED SERVICES, INCLUDING ANY DATA, ARE PROVIDED "AS IS," WITH ALL FAULTS, WITH NO REPRESENTATIONS OR WARRANTIES OF ANY KIND, EITHER EXPRESS OR IMPLIED, INCLUDING, BUT NOT LIMITED TO, ANY WARRANTIES OF MERCHANTABILITY, SATISFACTORY QUALITY, NON-INFRINGEMENT OR FITNESS FOR A PARTICULAR PURPOSE. YOU ASSUME TOTAL RESPONSIBILITY AND RISK FOR YOUR USE OF THIS SITE, ALL SITE-RELATED SERVICES, AND ANY THIRD PARTY WEBSITES OR APPLICATIONS. NO ORAL OR WRITTEN INFORMATION OR ADVICE SHALL CREATE A WARRANTY OF ANY KIND. ANY REFERENCES TO SPECIFIC PRODUCTS OR SERVICES ON THE WEBSITES DO NOT CONSTITUTE OR IMPLY A RECOMMENDATION OR ENDORSEMENT BY PACIFIC BIOSCIENCES.