{ "cells": [ { "cell_type": "code", "execution_count": 1, "metadata": { "ExecuteTime": { "end_time": "2018-03-18T15:03:52.561414Z", "start_time": "2018-03-18T15:03:52.389234Z" }, "collapsed": false, "deletable": true, "editable": true }, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ "\r\n", " USAGE:\r\n", "\r\n", "trim_galore [options] \r\n", "\r\n", "\r\n", "-h/--help Print this help message and exits.\r\n", "\r\n", "-v/--version Print the version information and exits.\r\n", "\r\n", "-q/--quality Trim low-quality ends from reads in addition to adapter removal. For\r\n", " RRBS samples, quality trimming will be performed first, and adapter\r\n", " trimming is carried in a second round. Other files are quality and adapter\r\n", " trimmed in a single pass. The algorithm is the same as the one used by BWA\r\n", " (Subtract INT from all qualities; compute partial sums from all indices\r\n", " to the end of the sequence; cut sequence at the index at which the sum is\r\n", " minimal). Default Phred score: 20.\r\n", "\r\n", "--phred33 Instructs Cutadapt to use ASCII+33 quality scores as Phred scores\r\n", " (Sanger/Illumina 1.9+ encoding) for quality trimming. Default: ON.\r\n", "\r\n", "--phred64 Instructs Cutadapt to use ASCII+64 quality scores as Phred scores\r\n", " (Illumina 1.5 encoding) for quality trimming.\r\n", "\r\n", "--fastqc Run FastQC in the default mode on the FastQ file once trimming is complete.\r\n", "\r\n", "--fastqc_args \"\" Passes extra arguments to FastQC. If more than one argument is to be passed\r\n", " to FastQC they must be in the form \"arg1 arg2 etc.\". An example would be:\r\n", " --fastqc_args \"--nogroup --outdir /home/\". Passing extra arguments will\r\n", " automatically invoke FastQC, so --fastqc does not have to be specified\r\n", " separately.\r\n", "\r\n", "-a/--adapter Adapter sequence to be trimmed. If not specified explicitly, Trim Galore will\r\n", " try to auto-detect whether the Illumina universal, Nextera transposase or Illumina\r\n", " small RNA adapter sequence was used. Also see '--illumina', '--nextera' and\r\n", " '--small_rna'. If no adapter can be detected within the first 1 million sequences\r\n", " of the first file specified Trim Galore defaults to '--illumina'.\r\n", "\r\n", "-a2/--adapter2 Optional adapter sequence to be trimmed off read 2 of paired-end files. This\r\n", " option requires '--paired' to be specified as well. If the libraries to be trimmed\r\n", " are smallRNA then a2 will be set to the Illumina small RNA 5' adapter automatically\r\n", " (GATCGTCGGACT).\r\n", "\r\n", "--illumina Adapter sequence to be trimmed is the first 13bp of the Illumina universal adapter\r\n", " 'AGATCGGAAGAGC' instead of the default auto-detection of adapter sequence.\r\n", "\r\n", "--nextera Adapter sequence to be trimmed is the first 12bp of the Nextera adapter\r\n", " 'CTGTCTCTTATA' instead of the default auto-detection of adapter sequence.\r\n", "\r\n", "--small_rna Adapter sequence to be trimmed is the first 12bp of the Illumina Small RNA 3' Adapter\r\n", " 'TGGAATTCTCGG' instead of the default auto-detection of adapter sequence. Selecting\r\n", " to trim smallRNA adapters will also lower the --length value to 18bp. If the smallRNA\r\n", " libraries are paired-end then a2 will be set to the Illumina small RNA 5' adapter\r\n", " automatically (GATCGTCGGACT) unless -a 2 had been defined explicitly.\r\n", "\r\n", "--max_length Discard reads that are longer than bp after trimming. This is only advised for\r\n", " smallRNA sequencing to remove non-small RNA sequences.\r\n", "\r\n", "\r\n", "--stringency Overlap with adapter sequence required to trim a sequence. Defaults to a\r\n", " very stringent setting of 1, i.e. even a single bp of overlapping sequence\r\n", " will be trimmed off from the 3' end of any read.\r\n", "\r\n", "-e Maximum allowed error rate (no. of errors divided by the length of the matching\r\n", " region) (default: 0.1)\r\n", "\r\n", "--gzip Compress the output file with GZIP. If the input files are GZIP-compressed\r\n", " the output files will automatically be GZIP compressed as well. As of v0.2.8 the\r\n", " compression will take place on the fly.\r\n", "\r\n", "--dont_gzip Output files won't be compressed with GZIP. This option overrides --gzip.\r\n", "\r\n", "--length Discard reads that became shorter than length INT because of either\r\n", " quality or adapter trimming. A value of '0' effectively disables\r\n", " this behaviour. Default: 20 bp.\r\n", "\r\n", " For paired-end files, both reads of a read-pair need to be longer than\r\n", " bp to be printed out to validated paired-end files (see option --paired).\r\n", " If only one read became too short there is the possibility of keeping such\r\n", " unpaired single-end reads (see --retain_unpaired). Default pair-cutoff: 20 bp.\r\n", "\r\n", "--max_n COUNT The total number of Ns (as integer) a read may contain before it will be removed altogether.\r\n", " In a paired-end setting, either read exceeding this limit will result in the entire\r\n", " pair being removed from the trimmed output files.\r\n", "\r\n", "--trim-n Removes Ns from either side of the read. This option does currently not work in RRBS mode.\r\n", "\r\n", "-o/--output_dir If specified all output will be written to this directory instead of the current\r\n", " directory.\r\n", "\r\n", "--no_report_file If specified no report file will be generated.\r\n", "\r\n", "--suppress_warn If specified any output to STDOUT or STDERR will be suppressed.\r\n", "\r\n", "--clip_R1 Instructs Trim Galore to remove bp from the 5' end of read 1 (or single-end\r\n", " reads). This may be useful if the qualities were very poor, or if there is some\r\n", " sort of unwanted bias at the 5' end. Default: OFF.\r\n", "\r\n", "--clip_R2 Instructs Trim Galore to remove bp from the 5' end of read 2 (paired-end reads\r\n", " only). This may be useful if the qualities were very poor, or if there is some sort\r\n", " of unwanted bias at the 5' end. For paired-end BS-Seq, it is recommended to remove\r\n", " the first few bp because the end-repair reaction may introduce a bias towards low\r\n", " methylation. Please refer to the M-bias plot section in the Bismark User Guide for\r\n", " some examples. Default: OFF.\r\n", "\r\n", "--three_prime_clip_R1 Instructs Trim Galore to remove bp from the 3' end of read 1 (or single-end\r\n", " reads) AFTER adapter/quality trimming has been performed. This may remove some unwanted\r\n", " bias from the 3' end that is not directly related to adapter sequence or basecall quality.\r\n", " Default: OFF.\r\n", "\r\n", "--three_prime_clip_R2 Instructs Trim Galore to remove bp from the 3' end of read 2 AFTER\r\n", " adapter/quality trimming has been performed. This may remove some unwanted bias from\r\n", " the 3' end that is not directly related to adapter sequence or basecall quality.\r\n", " Default: OFF.\r\n", "\r\n", "--path_to_cutadapt You may use this option to specify a path to the Cutadapt executable,\r\n", " e.g. /my/home/cutadapt-1.7.1/bin/cutadapt. Else it is assumed that Cutadapt is in\r\n", " the PATH.\r\n", "\r\n", "\r\n", "RRBS-specific options (MspI digested material):\r\n", "\r\n", "--rrbs Specifies that the input file was an MspI digested RRBS sample (recognition\r\n", " site: CCGG). Single-end or Read 1 sequences (paired-end) which were adapter-trimmed\r\n", " will have a further 2 bp removed from their 3' end. Sequences which were merely\r\n", " trimmed because of poor quality will not be shortened further. Read 2 of paired-end\r\n", " libraries will in addition have the first 2 bp removed from the 5' end (by setting \r\n", " '--clip_r2 2'). This is to avoid using artificial methylation calls from the filled-in\r\n", " cytosine positions close to the 3' MspI site in sequenced fragments. \r\n", " This option is not recommended for users of the NuGEN ovation RRBS System 1-16\r\n", " kit (see below).\r\n", "\r\n", "--non_directional Selecting this option for non-directional RRBS libraries will screen\r\n", " quality-trimmed sequences for 'CAA' or 'CGA' at the start of the read\r\n", " and, if found, removes the first two basepairs. Like with the option\r\n", " '--rrbs' this avoids using cytosine positions that were filled-in\r\n", " during the end-repair step. '--non_directional' requires '--rrbs' to\r\n", " be specified as well. Note that this option does not set '--clip_r2 2' in\r\n", " paired-end mode.\r\n", "\r\n", "--keep Keep the quality trimmed intermediate file. Default: off, which means\r\n", " the temporary file is being deleted after adapter trimming. Only has\r\n", " an effect for RRBS samples since other FastQ files are not trimmed\r\n", " for poor qualities separately.\r\n", "\r\n", "\r\n", "Note for RRBS using the NuGEN Ovation RRBS System 1-16 kit:\r\n", "\r\n", "Owing to the fact that the NuGEN Ovation kit attaches a varying number of nucleotides (0-3) after each MspI\r\n", "site Trim Galore should be run WITHOUT the option --rrbs. This trimming is accomplished in a subsequent \r\n", "diversity trimming step afterwards (see their manual).\r\n", "\r\n", "\r\n", "\r\n", "Note for RRBS using MseI:\r\n", "\r\n", "If your DNA material was digested with MseI (recognition motif: TTAA) instead of MspI it is NOT necessary\r\n", "to specify --rrbs or --non_directional since virtually all reads should start with the sequence\r\n", "'TAA', and this holds true for both directional and non-directional libraries. As the end-repair of 'TAA'\r\n", "restricted sites does not involve any cytosines it does not need to be treated especially. Instead, simply\r\n", "run Trim Galore! in the standard (i.e. non-RRBS) mode.\r\n", "\r\n", "\r\n", "\r\n", "\r\n", "Paired-end specific options:\r\n", "\r\n", "--paired This option performs length trimming of quality/adapter/RRBS trimmed reads for\r\n", " paired-end files. To pass the validation test, both sequences of a sequence pair\r\n", " are required to have a certain minimum length which is governed by the option\r\n", " --length (see above). If only one read passes this length threshold the\r\n", " other read can be rescued (see option --retain_unpaired). Using this option lets\r\n", " you discard too short read pairs without disturbing the sequence-by-sequence order\r\n", " of FastQ files which is required by many aligners.\r\n", "\r\n", " Trim Galore! expects paired-end files to be supplied in a pairwise fashion, e.g.\r\n", " file1_1.fq file1_2.fq SRR2_1.fq.gz SRR2_2.fq.gz ... .\r\n", "\r\n", "-t/--trim1 Trims 1 bp off every read from its 3' end. This may be needed for FastQ files that\r\n", " are to be aligned as paired-end data with Bowtie. This is because Bowtie (1) regards\r\n", " alignments like this:\r\n", "\r\n", " R1 ---------------------------> or this: -----------------------> R1\r\n", " R2 <--------------------------- <----------------- R2\r\n", "\r\n", " as invalid (whenever a start/end coordinate is contained within the other read).\r\n", " NOTE: If you are planning to use Bowtie2, BWA etc. you don't need to specify this option.\r\n", "\r\n", "--retain_unpaired If only one of the two paired-end reads became too short, the longer\r\n", " read will be written to either '.unpaired_1.fq' or '.unpaired_2.fq'\r\n", " output files. The length cutoff for unpaired single-end reads is\r\n", " governed by the parameters -r1/--length_1 and -r2/--length_2. Default: OFF.\r\n", "\r\n", "-r1/--length_1 Unpaired single-end read length cutoff needed for read 1 to be written to\r\n", " '.unpaired_1.fq' output file. These reads may be mapped in single-end mode.\r\n", " Default: 35 bp.\r\n", "\r\n", "-r2/--length_2 Unpaired single-end read length cutoff needed for read 2 to be written to\r\n", " '.unpaired_2.fq' output file. These reads may be mapped in single-end mode.\r\n", " Default: 35 bp.\r\n", "\r\n", "\r\n", "Last modified on 13 November 2017.\r\n", "\r\n" ] } ], "source": [ "!/Applications/bioinfo/TrimGalore-0.4.5/trim_galore --help" ] }, { "cell_type": "code", "execution_count": null, "metadata": { "collapsed": true, "deletable": true, "editable": true }, "outputs": [], "source": [] } ], "metadata": { "kernelspec": { "display_name": "Python 2", "language": "python", "name": "python2" }, "language_info": { "codemirror_mode": { "name": "ipython", "version": 2 }, "file_extension": ".py", "mimetype": "text/x-python", "name": "python", "nbconvert_exporter": "python", "pygments_lexer": "ipython2", "version": "2.7.12" } }, "nbformat": 4, "nbformat_minor": 2 }