umi_tools/umi_tools_extract

extract

umi-tools

umi

fastq

Description

Flexible removal of UMI sequences from fastq reads.
UMIs are removed and appended to the read name. Any other barcode, for example a library barcode,
is left on the read. Can also filter reads by quality or against a whitelist.

Input

Name	Type & Properties	Description
--input	file required	File containing the input data.
--read2_in	file	File containing the input data for the R2 reads (if paired). If provided, a <list of other required arguments> need to be provided.
--bc_pattern -p	string	The UMI barcode pattern to use e.g. 'NNNNNN' indicates that the first 6 nucleotides of the read are from the UMI.
--bc_pattern2	string	The UMI barcode pattern to use for read 2.

Name

Type & Properties

--input

file

required

--read2_in

file

--bc_pattern

-p

string

--bc_pattern2

string

Output

Name	Type & Properties	Description
--output	file required output	Output file for read 1.
--read2_out	file output	Output file for read 2.
--filtered_out	file	Write out reads not matching regex pattern or cell barcode whitelist to this file.
--filtered_out2	file	Write out read pairs not matching regex pattern or cell barcode whitelist to this file.

Name

Type & Properties

--output

file

required

output

--read2_out

file

output

--filtered_out

file

--filtered_out2

file

Extract Options

Name	Type & Properties	Description
--extract_method	string	UMI pattern to use. Default: `string`.
--error_correct_cell	boolean_true	Error correct cell barcodes to the whitelist.
--whitelist	file	Whitelist of accepted cell barcodes tab-separated format, where column 1 is the whitelisted cell barcodes and column 2 is the list (comma-separated) of other cell barcodes which should be corrected to the barcode in column 1. If the --error_correct_cell option is not used, this column will be ignored.
--blacklist	file	BlackWhitelist of cell barcodes to discard.
--subset_reads	integer	Only parse the first N reads.
--quality_filter_threshold	integer	Remove reads where any UMI base quality score falls below this threshold.
--quality_filter_mask	string	If a UMI base has a quality below this threshold, replace the base with 'N'.
--quality_encoding	string	Quality score encoding. Choose from: * phred33 [33-77] * phred64 [64-106] * solexa [59-106]
--reconcile_pairs	boolean_true	Allow read 2 infile to contain reads not in read 1 infile. This enables support for upstream protocols where read one contains cell barcodes, and the read pairs have been filtered and corrected without regard to the read2.
--three_prime --3prime	boolean_true	By default the barcode is assumed to be on the 5' end of the read, but use this option to sepecify that it is on the 3' end instead. This option only works with --extract_method=string since 3' encoding can be specified explicitly with a regex, e.g `.*(?P<umi_1>.{5})$`.
--ignore_read_pair_suffixes	boolean_true	Ignore "/1" and "/2" read name suffixes. Note that this options is required if the suffixes are not whitespace separated from the rest of the read name. arguments:
--umi_separator	string	The character that separates the UMI in the read name. Most likely a colon if you skipped the extraction with UMI-tools and used other software. Default: `_`
--grouping_method	string	Method to use to determine read groups by subsuming those with similar UMIs. All methods start by identifying the reads with the same mapping position, but treat similar yet nonidentical UMIs differently. Default: `directional`

Name

Type & Properties

--extract_method

string

--error_correct_cell

boolean_true

--whitelist

file

--blacklist

file

--subset_reads

integer

--quality_filter_threshold

integer

--quality_filter_mask

string

--quality_encoding

string

--reconcile_pairs

boolean_true

--three_prime

--3prime

boolean_true

--ignore_read_pair_suffixes

boolean_true

--umi_separator

string

--grouping_method

string

Common Options

Name	Type & Properties	Description
--log	file output	File with logging information.
--log2stderr	boolean_true	Send logging information to stderr.
--verbose	integer	Log level. The higher, the more output.
--error	file output	File with error information.
--temp_dir	string	Directory for temporary files. If not set, the bash environmental variable TMPDIR is used.
--compresslevel	integer	Level of Gzip compression to use. Default=6 matches GNU gzip rather than python gzip default (which is 9). Default `6`.
--timeit	file output	Store timing information in file.
--timeit_name	string	Name in timing file for this class of jobs.
--timeit_header	boolean_true	Add header for timing information.
--random_seed	integer	Random seed to initialize number generator with.

Name

Type & Properties

--log

file

output

--log2stderr

boolean_true

--verbose

integer

--error

file

output

--temp_dir

string

--compresslevel

integer

--timeit

file

output

--timeit_name

string

--timeit_header

boolean_true

--random_seed

integer

Run this component

Run the following command to execute this component with Nextflow:

cat > params.yaml <<'EOM'  
output: "$id.$key.output"  
read2_out: "$id.$key.read2_out"  
log: "$id.$key.log"  
error: "$id.$key.error"  
timeit: "$id.$key.timeit"  
timeit_name: [ "all" ]  
id: "run"  
publish_dir: "output/"  
EOM

nextflow run https://packages.viash-hub.com/vsh/biobox.git \  
  -revision v0.4.1 \  
  -main-script target/nextflow/umi_tools/umi_tools_extract/main.nf \  
  -params-file params.yaml

umi_tools/umi_tools_extract

Input

Output

Extract Options

Common Options

Run this component

Relationships

Used by

Uses