mbf-fastq-processor documentation

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

FilterByTag #

Remove sequences that have (or don’t have) a tag.

[[step]]
 action = "FilterByTag"
 label = "mytag"
 keep_or_remove = "Keep" # or "Remove"

This transformation filters reads based on the presence or absence of a specified tag. Use “Keep” to retain reads that have the tag, or “Remove” to discard reads that have the tag.

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

FilterByNumericTag #

Remove sequences that exceed thresholds on a numeric tag.


[[step]]
 action = "ExtractLength"
 label = "mytag"
 segment = "read1"

[[step]]
 action = "FilterByNumericTag"
 label = "mytag"
 keep_or_remove = "Keep" # or "Remove"
 min_value = 5 # >= this, optional
 max_value = 21 # < this, optional

The example only keeps reads that are between 5 and 20 bases long.

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

FilterByBoolTag #

Filter for sequences that have a boolean tag.

[[step]]
 action = "FilterByBoolTag"
 label = "mytag"
 keep_or_remove = "Keep" # or "Remove"

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

FilterEmpty #

[[step]]
 action = "FilterEmpty"
 segment = "read1" # Any of your input segments, or 'All'

Drop the molecule if the read has length 0. (Use after other processing.)

This get’s expanded to an internal tag and a FilteryByNumeric.

This is necessary if your modification can produce ’empty' reads - downstream aligners like STAR tend to dislike these in their input.

On segment=‘All’, only filters reads that are empty in all parts. Use multiple FilterEmpty steps to filter if any part is empty.

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

FilterSample #

[[step]]
 action = "FilterSample"
 p = 0.5 # float, the chance for any given read to be kept
 # 0..1
 seed = 42 # (optional) random seed for reproducibility

Randomly sample a percentage of reads. Requires a random seed to ensure reproducibility.