Iso-seq Tags

Tag Type Short Name Relevant Executable Value
CR string Cell Barcode correct Raw (uncorrected) cell barcode
CB string Cell Barcode correct Corrected cell barcode
UR string UMI None currently Raw UMI
UB string UMI None currently Corrected UMI
XM string UMI tag, correct Raw (after tag) or corrected (after correct) UMI
XC string Cell Barcode tag, correct Raw cell barcode
XA string tag name order tag, correct Order of tags names.
nc int Number of Candidates correct Number of candidate barcodes.
oc string Other Choices correct String representation of other potential barcodes.
gp int Group Passes correct Flag specifying whether or not the barcode for the given read passes filters. 1 for passing, 0 for failing.
nb int Barcode Distance correct Edit distance from the barcode for the read to the barcode to which it was reassigned. This is 0 if the barcode matches exactly, -1 if the barcode could not be rescued, and the edit distance otherwise.
rc int Real Cell correct Predicted real cell. This is 1 if a read is predicted to come from a real cell and 0 if predicted to be a non-real cell.
ic int input-consensus dedup, groupdedup Number of reads used to generate consensus. If less than is, this means that reads were down-sampled when consensus-calling.
is int input-sequences dedup, groupdedup Number of reads associated with isoform.
XO string X Overhang tag Overhang sequence tag.
XG string X GGG tag PacBio’s GGG UMI suffix tag
rq float read quality   Predicted accuracy for polished isoform
iz int maximum subreads used   maximum number of subreads used for polishing
it string trimmed tag List of barcodes/UMIs clipped during tag
im string names dedup, groupdedup List of names of input reads used in generating consensus

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