sc_trim_barcode: sc_trim_barcode

In LuyiTian/scPipe: Pipeline for single cell multi-omic data pre-processing

sc_trim_barcode

Description

Reformat fastq files so barcode and UMI sequences are moved from the sequence into the read name.

Usage

sc_trim_barcode(
  outfq,
  r1,
  r2 = NULL,
  read_structure = list(bs1 = -1, bl1 = 0, bs2 = 6, bl2 = 8, us = 0, ul = 6),
  filter_settings = list(rmlow = TRUE, rmN = TRUE, minq = 20, numbq = 2)
)

Arguments

outfq	the output fastq file, which reformat the barcode and UMI into the read name. Files ending in .gz will be automatically compressed.
r1	read one for pair-end reads. This read should contain the transcript.
r2	read two for pair-end reads, NULL if single read. (default: NULL)
read_structure	a list containing the read structure configuration: bs1: starting position of barcode in read one. -1 if no barcode in read one. bl1: length of barcode in read one, if there is no barcode in read one this number is used for trimming beginning of read one. bs2: starting position of barcode in read two bl2: length of barcode in read two us: starting position of UMI ul: length of UMI
filter_settings	A list contains read filter settings: rmlow whether to remove the low quality reads. rmN whether to remove reads that contains N in UMI or cell barcode. minq the minimum base pair quality that we allowed numbq the maximum number of base pair that have quality below numbq

Details

Positions used in this function are 0-indexed, so they start from 0 rather than 1. The default read structure in this function represents CEL-seq paired-ended reads. This contains a transcript in the first read, a UMI in the first 6bp of the second read followed by a 8bp barcode. So the read structure will be : list(bs1=-1, bl1=0, bs2=6, bl2=8, us=0, ul=6). bs1=-1, bl1=0 indicates negative start position and zero length for the barcode on read one, this is used to denote "no barcode" on read one. bs2=6, bl2=8 indicates there is a barcode in read two that starts at the 7th base with length 8bp. us=0, ul=6 indicates a UMI from first base of read two and the length in 6bp.

For a typical Drop-seq experiment the read structure will be list(bs1=-1, bl1=0, bs2=0, bl2=12, us=12, ul=8), which means the read one only contains transcript, the first 12bp in read two are cell barcode, followed by a 8bp UMI.

Value

generates a trimmed fastq file named outfq

Examples

data_dir="celseq2_demo"
## Not run: 
# for the complete workflow, refer to the vignettes
...
sc_trim_barcode(file.path(data_dir, "combined.fastq"),
   file.path(data_dir, "simu_R1.fastq"),
   file.path(data_dir, "simu_R2.fastq"))
...

## End(Not run)

LuyiTian/scPipe documentation built on Dec. 11, 2023, 8:21 p.m.