Quality and adapter trimmer of reads^[ACTGNactgn]*$^[ACTGNactgn]*$Instructs Trim Galore! to remove N bp from the 3' end of read 1 after adapter/quality trimming has been performed.
This may remove some unwanted bias from the 3' end that is not directly related to adapter sequence or basecall quality.
(--three_prime_clip_R1)Instructs Trim Galore! to remove N bp from the 3' end of read 2 after
adapter/quality trimming has been performed. This may remove some unwanted bias from
the 3' end that is not directly related to adapter sequence or basecall quality.cutadaptcutadapt
perl '$__tool_directory__/trim_galore' --version
$report_file;
#end if
]]>
Instructs Trim Galore! to remove N bp from the 3' end of read 1 after adapter/quality trimming has been performed.
This may remove some unwanted bias from the 3' end that is not directly related to adapter sequence or basecall quality.
(--three_prime_clip_R1)singlePaired['sPaired'] == "single"singlePaired['sPaired'] == "paired_collection"params['settingsType'] == "custom"params['retain_unpaired']['retain_unpaired_select'] == "retain_unpaired_output"singlePaired['sPaired'] == "paired_collection"singlePaired['sPaired'] == "paired"singlePaired['sPaired'] == "paired"params['settingsType'] == "custom"params['retain_unpaired']['retain_unpaired_select'] == "retain_unpaired_output"singlePaired['sPaired'] == "paired"params['settingsType'] == "custom"params['retain_unpaired']['retain_unpaired_select'] == "retain_unpaired_output"singlePaired['sPaired'] == "paired"params['settingsType'] == "custom"params['report'] == True
bp from the 3' end**
| Instructs Trim Galore to remove bp from the 3' end of read 1 (or single-end reads) AFTER adapter/quality trimming has been performed. This may remove some unwanted bias from the 3' end that is not directly related to adapter sequence or basecall quality. Default: OFF.
|
| *option --three_prime_clip_R1*
* **If Paired-End Reads**
* **Trims 1 bp off every read from its 3' end**
| This may be needed for FastQ files that are to be aligned as paired-end data with Bowtie. This is because Bowtie (1) regards alignments like this:
|
| R1 --------------------------->
| R2 <---------------------------
|
| or this:
|
| R1 ----------------------->
| R2 <-----------------
|
| as invalid (whenever a start/end coordinate is contained within the other read).
|
| *option --t*
* **Remove bp from the 3' end of read 1**
| Instructs Trim Galore to remove bp from the 3' end of read 1 (or single-end reads) AFTER adapter/quality trimming has been performed. This may remove some unwanted bias from the 3' end that is not directly related to adapter sequence or basecall quality. Default: OFF.
|
| *option --three_prime_clip_R1*
* **Remove bp from the 3' end of read 2**
| Instructs Trim Galore to remove bp from the 3' end of read 2 AFTER adapter/quality trimming has been performed. This may remove some unwanted bias from the 3' end that is not directly related to adapter sequence or basecall quality. Default: OFF.
|
| *option --three_prime_clip_R2*
----
**Advanced Settings**
* **Trim low-quality ends from reads in addition to adapter removal**
| For RRBS samples, quality trimming will be performed first, and adapter trimming is carried in a second round. Other files are quality and adapter trimmed in a single pass. The algorithm is the same as the one used by BWA (Subtract from all qualities; compute partial sums from all indices to the end of the sequence; cut sequence at the index at which the sum is minimal). Default Phred score: 20.
|
| *option -q*
* **Overlap with adapter sequence required to trim a sequence**
| Defaults to a very stringent setting of '1', i.e. even a single bp of overlapping sequence will be trimmed of the 3' end of any read.
|
| *option -s*
* **Maximum allowed error rate**
| (no. of errors divided by the length of the matching region) (default: 0.1).
|
| *option -e*
* **Discard reads that became shorter than length **
| because of either quality or adapter trimming. A value of '0' effectively disables this behaviour. Default: 20 bp.
|
| For paired-end files, both reads of a read-pair need to be longer than bp to be printed out to validated paired-end files (see option --paired). If only one read became too short there is the possibility of keeping such unpaired single-end reads (see --retain_unpaired). Default pair-cutoff: 20 bp.
|
| *option --length*
* **Instructs Trim Galore! to remove INT bp from the 5' end of read 1**
| Instructs Trim Galore to remove bp from the 5' end of read 1 (or single-end reads). This may be useful if the qualities were very poor, or if there is some sort of unwanted bias at the 5' end. Default: OFF.
|
| *option --clip_R1*
* **Instructs Trim Galore! to remove INT bp from the 5' end of read 2**
| Instructs Trim Galore to remove bp from the 5' end of read 2 (paired-end reads only). This may be useful if the qualities were very poor, or if there is some sort of unwanted bias at the 5' end. For paired-end BS-Seq, it is recommended to remove the first few bp because the end-repair reaction may introduce a bias towards low methylation. Please refer to the M-bias plot section in the Bismark User Guide for some examples. Default: OFF.
|
| *option --clip_R2*
* **Specify if you would like to retain unpaired reads**
| If only one of the two paired-end reads became too short, the longer read will be written to either '.unpaired_1.fq' or '.unpaired_2.fq' output files. The length cutoff for unpaired single-end reads is governed by the parameters -r1/--length_1 and -r2/--length_2. Default: OFF.
|
| *option --retained_unpaired*
----
**RRBS specific settings**
* **Specifies that the input file was an MspI digested RRBS sample (recognition site: CCGG)**
| Sequences which were adapter-trimmed will have a further 2 bp removed from their 3' end. This is to avoid that the filled-in C close to the second MspI site in a sequence is used for methylation calls. Sequences which were merely trimmed because of poor quality will not be shortened further.
|
| *option -rrbs*
* **Screen quality-trimmed sequences for 'CAA' or 'CGA' at the start of the read and, if found, removes the first two basepairs**
| Selecting this option for non-directional RRBS libraries will screen quality-trimmed sequences for 'CAA' or 'CGA' at the start of the read and, if found, removes the first two basepairs. Like with the option '--rrbs' this avoids using cytosine positions that were filled-in during the end-repair step. '--non_directional' requires '--rrbs' to be specified as well.
|
| *option --non_directional*]]>