Tag Usage on mbf-fastq-processor documentation

Mon, 01 Jan 0001 00:00:00 +0000

ForgetTag #

Forget about a tag. Useful if you want to store tags in a table, but not this one.

[[step]]
 action = "ForgetTag"
 label = "mytag"

This transformation removes a specified tag from the molecule’s tag collection.

Mon, 01 Jan 0001 00:00:00 +0000

StoreTagInComment #

Store currently present tags as comments on read names.

[[step]]
 action = "StoreTagInComment"
 label = "mytag" # if set, only store this tag
 segment = "read1" # Any of your input segments, or 'All'
 comment_insert_char = " " # (optional) char at which to insert comments
 comment_separator = "|" # (optional) char to separate comments
 region_separator = "_" # (optional) char to separate regions in a tag, if it has multiple

Comments are key=value pairs, separated by comment_separator which defaults to ‘|’. They get inserted at the first comment_insert_char, which defaults to space.

Mon, 01 Jan 0001 00:00:00 +0000

StoreTagInSequence #

Store the tag’s replacement in the sequence, replacing the original sequence at that location.

[[step]]
 action = "StoreTagInSequence"
 label = "mytag"
 ignore_missing = true # if false, an error is raised if the tag is missing

This transformation stores the tag’s value back into the sequence, replacing the original sequence at that location.

Mon, 01 Jan 0001 00:00:00 +0000

StoreTagLocationInComment #

Store the coordinates of a tag in the comment (start-end, 0-based, half-open).

[[step]]
 action = "StoreTagLocationInComment"
 label = "mytag"
 segment = "read1" # Any of your input segments, or 'All'
 comment_insert_char = " " # (optional) char at which to insert comments
 comment_separator = "|" # (optional) char to separate comments

This transformation stores the location coordinates of a tag as a comment in the read name, useful for tracking where tags were extracted from.

Mon, 01 Jan 0001 00:00:00 +0000

StoreTagsInTable #

Store the tags in a TSV table.

[[step]]
 action = "StoreTagsInTable"
 table_filename = "tags.tsv"
 compression = "Raw" # Raw, Gzip, Zstd
 region_separator = "_" # (optional) char to separate regions in a tag, if it has multiple

This transformation writes all current tags to a tab-separated values (TSV) table file for further analysis.

Mon, 01 Jan 0001 00:00:00 +0000

StoreTagInFastQ #

## Store the content of a tag in a fastq file.
## Needs a 'location 'tag'.
## Can store other tags in the read name.
## quality scores are set to '~'.
# [[step]]
# action = "StoreTagInFastQ"
# label = "mytag" # ${output.prefix}.tag.mytag.fq${.suffix_from_format}
# format = "Raw" # Raw, Gzip, Zstd
## compression_level = 6 # (optional) compression level for gzip (0-9) or zstd (1-22)
						 # defaults: gzip=6, zstd=5
# comment_tags = []# e.g. ["other_tag"] # see StoreTagInComment
# comment_location_tags = ["mytag"] # (optional) tags to add location info for, defaults to [label]
# # set to [] to disable location tracking
# comment_insert_char = ' ' # (optional) char at which to insert comments
# comment_separator = '|' # (optional) char to separate comments
# region_separator = "_" # (optional) char to separate regions in a tag, if it has multiple

Store the sequence of a tag in a fastq file, with other tags optionally stored in the read name as comments.

Mon, 01 Jan 0001 00:00:00 +0000

HammingCorrect #

Correct a tag to one of a predefined set of ‘barcodes’ using closest hamming distance.

[[step]]
 action = "HammingCorrect"
 label_in = "extracted_tag"
 label_out = "corrected_tag"
 barcodes = "mybarcodelist"
 max_hamming_distance = 1
 on_no_match = 'remove' # 'remove', 'empty', 'keep'

[barcodes.mybarcodelist]
 "AAAA" = "ignored" # only read when demultiplexing

on_no_match controls what happens if the tag cannot be corrected within the max_hamming_distance:

remove: Remove the hit (location and sequence), useful for FilterByTag later.
keep: Keep the original tag (and location)
empty: Keep the original location, but set the tag to empty.