umi_tools/umi_tools_dedup

umi_tools

deduplication

dedup

Description

Deduplicate reads based on the mapping co-ordinate and the UMI attached to the read.

Type

bash_script

License

MIT

Keywords

umi_tools

deduplication

dedup

Links

Repository

Documentation

Contributors

Launch

Run this component

Run the following command to execute this component with Nextflow:

cat > params.yaml <<'EOM'  
output: "$id.$key.output"  
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_dedup/main.nf \  
  -params-file params.yaml

Inputs

Name	Type & Properties	Description
--input --stdin	file required	Input BAM or SAM file. Use --in_sam to specify SAM format.
--in_sam	boolean_true	By default, inputs are assumed to be in BAM format. Use this options to specify the use of SAM format for input.
--bai	file	BAM index
--random_seed	integer	Random seed to initialize number generator with.

Name

Type & Properties

--input

--stdin

file

required

--in_sam

boolean_true

--bai

file

--random_seed

integer

Outputs

Name	Type & Properties	Description
--output --stdout	file required output	Deduplicated BAM file.
--out_sam	boolean_true	By default, outputa are written in BAM format. Use this options to specify the use of SAM format for output.
--paired	boolean_true	BAM is paired end - output both read pairs. This will also force the use of the template length to determine reads with the same mapping coordinates.
--output_stats	string	Generate files containing UMI based deduplication statistics files with this prefix in the file names.
--extract_umi_method	string	Specify the method by which the barcodes were encoded in the read. The options are: * read_id (default) * tag * umis
--umi_tag	string	The tag containing the UMI sequence. This is only required if the extract_umi_method is set to tag.
--umi_separator	string	The separator used to separate the UMI from the read sequence. This is only required if the extract_umi_method is set to id_read. Default: `_`.
--umi_tag_split	string	Separate the UMI in tag by <SPLIT> and take the first element.
--umi_tag_delimiter	string	Separate the UMI in by <DELIMITER> and concatenate the elements.
--cell_tag	string	The tag containing the cell barcode sequence. This is only required if the extract_umi_method is set to tag.
--cell_tag_split	string	Separate the cell barcode in tag by <SPLIT> and take the first element.
--cell_tag_delimiter	string	Separate the cell barcode in by <DELIMITER> and concatenate the elements.

Name

Type & Properties

--output

--stdout

file

required

output

--out_sam

boolean_true

--paired

boolean_true

--output_stats

string

--extract_umi_method

string

--umi_tag

string

--umi_separator

string

--umi_tag_split

string

--umi_tag_delimiter

string

--cell_tag

string

--cell_tag_split

string

--cell_tag_delimiter

string

Grouping Options

Name	Type & Properties	Description
--method	string	The method to use for grouping reads. The options are: * unique * percentile * cluster * adjacency * directional (default)
--edit_distance_threshold	integer	For the adjacency and cluster methods the threshold for the edit distance to connect two UMIs in the network can be increased. The default value of 1 works best unless the UMI is very long (>14bp). Default: `1`.
--spliced_is_unique	boolean_true	Causes two reads that start in the same position on the same strand and having the same UMI to be considered unique if one is spliced and the other is not. (Uses the 'N' cigar operation to test for splicing).
--soft_clip_threshold	integer	Mappers that soft clip will sometimes do so rather than mapping a spliced read if there is only a small overhang over the exon junction. By setting this option, you can treat reads with at least this many bases soft-clipped at the 3' end as spliced. Default: `4`.
--multimapping_detection_method	string	If the sam/bam contains tags to identify multimapping reads, you can specify for use when selecting the best read at a given loci. Supported tags are `NH`, `X0` and `XT`. If not specified, the read with the highest mapping quality will be selected.
--read_length	boolean_true	Use the read length as a criteria when deduping, for e.g. sRNA-Seq.

Name

Type & Properties

--method

string

--edit_distance_threshold

integer

--spliced_is_unique

boolean_true

--soft_clip_threshold

integer

--multimapping_detection_method

string

--read_length

boolean_true

Single-cell RNA-Seq Options

Name	Type & Properties	Description
--per_gene	boolean_true	Reads will be grouped together if they have the same gene. This is useful if your library prep generates PCR duplicates with non identical alignment positions such as CEL-Seq. Note this option is hardcoded to be on with the count command. I.e. counting is always performed per-gene. Must be combined with either --gene_tag or --per_contig option.
--gene_tag	string	Deduplicate per gene. The gene information is encoded in the bam read tag specified.
--assigned_status_tag	string	BAM tag which describes whether a read is assigned to a gene. Defaults to the same value as given for --gene_tag.
--skip_tags_regex	string	Use in conjunction with the --assigned_status_tag option to skip any reads where the tag matches this regex. Default ("^[__\|Unassigned]") matches anything which starts with "__" or "Unassigned".
--per_contig	boolean_true	Deduplicate per contig (field 3 in BAM; RNAME). All reads with the sam contig will be considered to have the same alignment position. This is useful if you have aligned to a reference transcriptome with one transcript per gene. If you have aligned to a transcriptome with more than one transcript per gene, you can supply a map between transcripts and gene using the --gene_transcript_map option.
--gene_transcript_map	file	A file containing a mapping between gene names and transcript names. The file should be tab separated with the gene name in the first column and the transcript name in the second column.
--per_cell	boolean_true	Reads will only be grouped together if they have the same cell barcode. Can be combined with --per_gene.

Name

Type & Properties

--per_gene

boolean_true

--gene_tag

string

--assigned_status_tag

string

--skip_tags_regex

string

--per_contig

boolean_true

--gene_transcript_map

file

--per_cell

boolean_true

SAM/BAM Options

Name	Type & Properties	Description
--mapping_quality	integer	Minimium mapping quality (MAPQ) for a read to be retained. Default: `0`.
--unmapped_reads	string	How unmapped reads should be handled. The options are: * "discard": Discard all unmapped reads. (default) * "use": If read2 is unmapped, deduplicate using read1 only. Requires --paired. * "output": Output unmapped reads/read pairs without UMI grouping/deduplication. Only available in umi_tools group.
--chimeric_pairs	string	How chimeric pairs should be handled. The options are: * "discard": Discard all chimeric read pairs. * "use": Deduplicate using read1 only. (default) * "output": Output chimeric pairs without UMI grouping/deduplication. Only available in umi_tools group.
--unpaired_reads	string	How unpaired reads should be handled. The options are: * "discard": Discard all unmapped reads. * "use": If read2 is unmapped, deduplicate using read1 only. Requires --paired. (default) * "output": Output unmapped reads/read pairs without UMI grouping/deduplication. Only available in umi_tools group.
--ignore_umi	boolean_true	Ignore the UMI and group reads using mapping coordinates only.
--subset	double	Only consider a fraction of the reads, chosen at random. This is useful for doing saturation analyses.
--chrom	string	Only consider a single chromosome. This is useful for debugging/testing purposes.

Name

Type & Properties

--mapping_quality

integer

--unmapped_reads

string

--chimeric_pairs

string

--unpaired_reads

string

--ignore_umi

boolean_true

--subset

double

--chrom

string

Group/Dedup Options

Name	Type & Properties	Description
--no_sort_output	boolean_true	By default, output is sorted. This involves the use of a temporary unsorted file (saved in --temp_dir). Use this option to turn off sorting.
--buffer_whole_contig	boolean_true	Forces dedup to parse an entire contig before yielding any reads for deduplication. This is the only way to absolutely guarantee that all reads with the same start position are grouped together for deduplication since dedup uses the start position of the read, not the alignment coordinate on which the reads are sorted. However, by default, dedup reads for another 1000bp before outputting read groups which will avoid any reads being missed with short read sequencing (<1000bp).

Name

Type & Properties

--no_sort_output

boolean_true

--buffer_whole_contig

boolean_true

Common Options

Name	Type & Properties	Description
--log -L	file	File with logging information.
--log2stderr	boolean_true	Send logging information to stderr.
--verbose -v	integer	Log level. The higher, the more output. Default: `0`.
--error -E	file	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. Default: `6`.
--timeit	file	Store timing information in file.
--timeit_name	string	Name in timing file for this class of jobs. Default: `all`.
--timeit_header	string	Add header for timing information.

Name

Type & Properties

--log

-L

file

--log2stderr

boolean_true

--verbose

-v

integer

--error

-E

file

--temp_dir

string

--compresslevel

integer

--timeit

file

--timeit_name

string

--timeit_header

string