Rationale:
Trimmomatic trims adapters from the ends of sequencing reads, and
optionally, crops nucleotides from the ends of the trimmed
reads based on quality or length criteria.
Where:
Run Trimmomatic in the same folder as your read files.
Input:
RNAseq reads: Before opening this menu, select RNA-seq
readfiles to be mapped to the genome. For paired-end reads,
Trimmomatic works with pair of files. Files can be selected in
pairs using File --> guesspairs.py.
Input read files
may be gzipped or uncompressed.
Parameters:
Because of the large number of parameters for Trimmomatic, it is
essential to consult the Trimmomatic
User's Guide to make an informed decision as to how adapter
clipping and/or cropping should be done.
Trimmomatic specifies a number of trimming steps:
- ILLUMINACLIP: Cut
adapter and other illumina-specific sequences from the read.
- SLIDINGWINDOW:
Performs a sliding window trimming approach. It starts
- scanning at the 5‟
end and clips the read once the average quality within the
window
- falls below a
threshold.
- MAXINFO: An adaptive
quality trimmer which balances read length and error rate to
- maximise the value
of each read
- LEADING: Cut bases
off the start of a read, if below a threshold quality
- TRAILING: Cut bases
off the end of a read, if below a threshold quality
- CROP: Cut the read
to a specified length by removing bases from the end
- HEADCROP: Cut the
specified number of bases from the start of the read
- MINLEN: Drop the
read if it is below a specified length
- AVGQUAL: Drop the
read if the average quality is below the specified level
- TOPHRED33: Convert
quality scores to Phred-33 (not implemented in blreads)
- TOPHRED64: Convert
quality scores to Phred-64 (not implemented in blreads)
These may be done in any
order, but in most cases ILLUMINACLIP should be the first step.
The blreads menu for Trimmomatic allows the user to turn steps on
and off, and specify a rank, which tells the order in which the
steps should be done.
By default, ILLUMINACLIP is turned on, and all other steps are
turned off.
Parameters are found in four tabs of the
Trimmomatic menu.
General
- Parameters CPU usage, output and email notification
Clipadapt -
Settings for the ILLUMINACLIP step.
Quality -
Settings for trimming reads based on quality of bases
Cropping -
Settings for cropping reads to a given length, or cropping
nucleotides from the ends.
MINLEN
- This parameter is included in the Cropping menu, but
actually specifies the minimal length for final trimmed reads
to be written to the output. If chosen, this step is done
last, after all other steps.
Output:
Name for output directory - This defaults to a
directory in the parent directory. It is usually the best
organizational practice for the paired and single read files to go
somewhere other than the current directory.
Output files will be the names of the original fastq files. For
each pair of paired end read files, the basename will be extended
with _1P and _1U for paired and unpaired reads generated from the
forward read file, and _2P and _2U for paired and unpaired reads
generated from the reverse read file. Trimmed reads from
single-end files will have _S added to the basename.
A new blreads window will be opened in the output directory.