Tag Usage on mbf-fastq-processor documentation

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

ForgetAllTags #

Remove every tag currently stored for the read batch.

[[step]]
 action = "ForgetAllTags"

Use this when you want to clear all tag labels before continuing. It is handy after persisting tags to an external table, or before running steps that must not see previously extracted metadata.

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"
 in_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"
 in_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 before 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"
 in_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.

Note that if this changes the length of the sequence, existing location tags will loose their location data (retaining their sequence though).

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"
 in_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"
 infix = "tags"
 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.

The output filename is constructed as {prefix}_{infix}.tsv (or with custom separator if configured).

Interaction with demultiplexing #

When demultiplexing is used, separate TSV files are created for each barcode: {prefix}_{infix}_{barcode}.tsv.

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 '~'.
# With demultiplexing: creates separate files per barcode
 [[step]]
 action = "StoreTagInFastQ"
 in_label = "mytag" # tag to store. If no infix is set, infix = tag={in_label}
 format = "Fastq" # FASTQ / FASTA / BAm
 compression = "gz" # or "zstd" | "none" # (optional) compression format, not if format == BAM
 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 [in_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"
 in_label = "mytag"
 out_label = "my_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.