getScReads: merge into MTseeker; could also do this with SmartSeq, etc.

In trichelab/MTseeker: Bioconductor Tools for Human Mitochondrial Variant Analysis

Description

For 10X BAMs, cellTag is CB and fragTag is UB. For Salmon BAMs, cellTag is CB and fragTag is UR. For BioRad BAMs, cellTag is DB and fragTag is XB (I think). Per-cell pileups can be generated directly from BAMs, though this is tricky. I'm not 100 percent sure how to deal with UMI reconciliation above, though.

Usage

getScReads(
  BAM,
  cellTag = "CB",
  fragTag = "UB",
  tagFilt = NULL,
  dedupe = FALSE,
  MTonly = FALSE,
  byCell = FALSE,
  byFrag = FALSE
)

Arguments

BAM	a BAM file or a BamFile object
cellTag	what tag to use for cell identification (CB)
fragTag	what tag to use for fragment identification (UB)
tagFilt	optional tag filter (eg. list(CB="ATCGATCGAT-1")) (NULL)
dedupe	drop reads with missing or duplicate (CB,UB)? (FALSE)
MTonly	only reaad in mitochondrial reads? (FALSE)
byCell	split by cell? (FALSE; only set TRUE for MT)
byFrag	split by fragment? (FALSE; only set TRUE for MT)

Value

         a GAlignments or GAlignmentsList (if byCell/byFrag)

trichelab/MTseeker documentation built on March 8, 2021, 6:20 p.m.