安装
(rnaseq) root 11:58:44 ~
$ conda install -y trim-galoretrim-galore
Collecting package metadata (current_repodata.json): done
Solving environment: done
==> WARNING: A newer version of conda exists. <==
current version: 4.9.2
latest version: 4.10.1
Please update conda by running
$ conda update -n base -c defaults conda
## Package Plan ##
environment location: /root/miniconda3/envs/rnaseq
added / updated specs:
- trim-galore
The following packages will be downloaded:
package | build
---------------------------|-----------------
cutadapt-3.4 | py39h38f01e4_1 198 KB https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/bioconda
dnaio-0.5.1 | py39h38f01e4_0 140 KB https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/bioconda
isa-l-2.30.0 | ha770c72_4 192 KB https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
pigz-2.6 | h27826a3_0 87 KB https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
python-isal-0.10.0 | py39h3811e60_0 117 KB https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
trim-galore-0.6.6 | hdfd78af_1 42 KB https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/bioconda
xopen-1.1.0 | py39hf3d152e_2 20 KB https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
------------------------------------------------------------
Total: 797 KB
The following NEW packages will be INSTALLED:
cutadapt anaconda/cloud/bioconda/linux-64::cutadapt-3.4-py39h38f01e4_1
dnaio anaconda/cloud/bioconda/linux-64::dnaio-0.5.1-py39h38f01e4_0
isa-l anaconda/cloud/conda-forge/linux-64::isa-l-2.30.0-ha770c72_4
pigz anaconda/cloud/conda-forge/linux-64::pigz-2.6-h27826a3_0
python-isal anaconda/cloud/conda-forge/linux-64::python-isal-0.10.0-py39h3811e60_0
trim-galore anaconda/cloud/bioconda/noarch::trim-galore-0.6.6-hdfd78af_1
xopen anaconda/cloud/conda-forge/linux-64::xopen-1.1.0-py39hf3d152e_2
Downloading and Extracting Packages
python-isal-0.10.0 | 117 KB | ######################################## | 100%
trim-galore-0.6.6 | 42 KB | ######################################## | 100%
xopen-1.1.0 | 20 KB | ######################################## | 100%
dnaio-0.5.1 | 140 KB | ######################################## | 100%
pigz-2.6 | 87 KB | ######################################## | 100%
isa-l-2.30.0 | 192 KB | ######################################## | 100%
cutadapt-3.4 | 198 KB | ######################################## | 100%
Preparing transaction: done
Verifying transaction: done
Executing transaction: done
(rnaseq) root 12:00:42 ~
查看
(rnaseq) root 12:05:52 ~
$ cutadapt --help
cutadapt version 3.4
Copyright (C) 2010-2021 Marcel Martin
cutadapt removes adapter sequences from high-throughput sequencing reads.
Usage:
cutadapt -a ADAPTER [options] [-o output.fastq] input.fastq
For paired-end reads:
cutadapt -a ADAPT1 -A ADAPT2 [options] -o out1.fastq -p out2.fastq in1.fastq in2.fastq
Replace "ADAPTER" with the actual sequence of your 3' adapter. IUPAC wildcard
characters are supported. All reads from input.fastq will be written to
output.fastq with the adapter sequence removed. Adapter matching is
error-tolerant. Multiple adapter sequences can be given (use further -a
options), but only the best-matching adapter will be removed.
Input may also be in FASTA format. Compressed input and output is supported and
auto-detected from the file name (.gz, .xz, .bz2). Use the file name '-' for
standard input/output. Without the -o option, output is sent to standard output.
Citation:
Marcel Martin. Cutadapt removes adapter sequences from high-throughput
sequencing reads. EMBnet.Journal, 17(1):10-12, May 2011.
http://dx.doi.org/10.14806/ej.17.1.200
Run "cutadapt --help" to see all command-line options.
See https://cutadapt.readthedocs.io/ for full documentation.
Options:
-h, --help Show this help message and exit
--version Show version number and exit
--debug Print debug log. Use twice to also print DP matrices
-j CORES, --cores CORES
Number of CPU cores to use. Use 0 to auto-detect. Default:
1
Finding adapters:
Parameters -a, -g, -b specify adapters to be removed from each read (or from
the first read in a pair if data is paired). If specified multiple times, only
the best matching adapter is trimmed (but see the --times option). When the
special notation 'file:FILE' is used, adapter sequences are read from the given
FASTA file.
-a ADAPTER, --adapter ADAPTER
Sequence of an adapter ligated to the 3' end (paired data:
of the first read). The adapter and subsequent bases are
trimmed. If a '$' character is appended ('anchoring'), the
adapter is only found if it is a suffix of the read.
-g ADAPTER, --front ADAPTER
Sequence of an adapter ligated to the 5' end (paired data:
of the first read). The adapter and any preceding bases are
trimmed. Partial matches at the 5' end are allowed. If a
'^' character is prepended ('anchoring'), the adapter is
only found if it is a prefix of the read.
-b ADAPTER, --anywhere ADAPTER
Sequence of an adapter that may be ligated to the 5' or 3'
end (paired data: of the first read). Both types of matches
as described under -a and -g are allowed. If the first base
of the read is part of the match, the behavior is as with
-g, otherwise as with -a. This option is mostly for
rescuing failed library preparations - do not use if you
know which end your adapter was ligated to!
-e E, --error-rate E, --errors E
Maximum allowed error rate (if 0 <= E < 1), or absolute
number of errors for full-length adapter match (if E is an
integer >= 1). Error rate = no. of errors divided by length
of matching region. Default: 0.1 (10%)
--no-indels Allow only mismatches in alignments. Default: allow both
mismatches and indels
-n COUNT, --times COUNT
Remove up to COUNT adapters from each read. Default: 1
-O MINLENGTH, --overlap MINLENGTH
Require MINLENGTH overlap between read and adapter for an
adapter to be found. Default: 3
--match-read-wildcards
Interpret IUPAC wildcards in reads. Default: False
-N, --no-match-adapter-wildcards
Do not interpret IUPAC wildcards in adapters.
--action {trim,retain,mask,lowercase,none}
What to do if a match was found. trim: trim adapter and up-
or downstream sequence; retain: trim, but retain adapter;
mask: replace with 'N' characters; lowercase: convert to
lowercase; none: leave unchanged. Default: trim
--rc, --revcomp Check both the read and its reverse complement for adapter
matches. If match is on reverse-complemented version,
output that one. Default: check only read
Additional read modifications:
-u LENGTH, --cut LENGTH
Remove bases from each read (first read only if paired). If
LENGTH is positive, remove bases from the beginning. If
LENGTH is negative, remove bases from the end. Can be used
twice if LENGTHs have different signs. This is applied
*before* adapter trimming.
--nextseq-trim 3'CUTOFF
NextSeq-specific quality trimming (each read). Trims also
dark cycles appearing as high-quality G bases.
-q [5'CUTOFF,]3'CUTOFF, --quality-cutoff [5'CUTOFF,]3'CUTOFF
Trim low-quality bases from 5' and/or 3' ends of each read
before adapter removal. Applied to both reads if data is
paired. If one value is given, only the 3' end is trimmed.
If two comma-separated cutoffs are given, the 5' end is
trimmed with the first cutoff, the 3' end with the second.
--quality-base N Assume that quality values in FASTQ are encoded as
ascii(quality + N). This needs to be set to 64 for some old
Illumina FASTQ files. Default: 33
--length LENGTH, -l LENGTH
Shorten reads to LENGTH. Positive values remove bases at
the end while negative ones remove bases at the beginning.
This and the following modifications are applied after
adapter trimming.
--trim-n Trim N's on ends of reads.
--length-tag TAG Search for TAG followed by a decimal number in the
description field of the read. Replace the decimal number
with the correct length of the trimmed read. For example,
use --length-tag 'length=' to correct fields like
'length=123'.
--strip-suffix STRIP_SUFFIX
Remove this suffix from read names if present. Can be given
multiple times.
-x PREFIX, --prefix PREFIX
Add this prefix to read names. Use {name} to insert the
name of the matching adapter.
-y SUFFIX, --suffix SUFFIX
Add this suffix to read names; can also include {name}
--rename TEMPLATE Rename reads using TEMPLATE containing variables such as
{id}, {adapter_name} etc. (see documentation)
--zero-cap, -z Change negative quality values to zero.
Filtering of processed reads:
Filters are applied after above read modifications. Paired-end reads are always
discarded pairwise (see also --pair-filter).
-m LEN[:LEN2], --minimum-length LEN[:LEN2]
Discard reads shorter than LEN. Default: 0
-M LEN[:LEN2], --maximum-length LEN[:LEN2]
Discard reads longer than LEN. Default: no limit
--max-n COUNT Discard reads with more than COUNT 'N' bases. If COUNT is a
number between 0 and 1, it is interpreted as a fraction of
the read length.
--max-expected-errors ERRORS, --max-ee ERRORS
Discard reads whose expected number of errors (computed
from quality values) exceeds ERRORS.
--discard-trimmed, --discard
Discard reads that contain an adapter. Use also -O to avoid
discarding too many randomly matching reads.
--discard-untrimmed, --trimmed-only
Discard reads that do not contain an adapter.
--discard-casava Discard reads that did not pass CASAVA filtering (header
has :Y:).
Output:
--quiet Print only error messages.
--report {full,minimal}
Which type of report to print: 'full' or 'minimal'.
Default: full
-o FILE, --output FILE
Write trimmed reads to FILE. FASTQ or FASTA format is
chosen depending on input. Summary report is sent to
standard output. Use '{name}' for demultiplexing (see
docs). Default: write to standard output
--fasta Output FASTA to standard output even on FASTQ input.
-Z Use compression level 1 for gzipped output files (faster,
but uses more space)
--info-file FILE Write information about each read and its adapter matches
into FILE. See the documentation for the file format.
-r FILE, --rest-file FILE
When the adapter matches in the middle of a read, write the
rest (after the adapter) to FILE.
--wildcard-file FILE When the adapter has N wildcard bases, write adapter bases
matching wildcard positions to FILE. (Inaccurate with
indels.)
--too-short-output FILE
Write reads that are too short (according to length
specified by -m) to FILE. Default: discard reads
--too-long-output FILE
Write reads that are too long (according to length
specified by -M) to FILE. Default: discard reads
--untrimmed-output FILE
Write reads that do not contain any adapter to FILE.
Default: output to same file as trimmed reads
Paired-end options:
The -A/-G/-B/-U options work like their -a/-b/-g/-u counterparts, but are
applied to the second read in each pair.
-A ADAPTER 3' adapter to be removed from second read in a pair.
-G ADAPTER 5' adapter to be removed from second read in a pair.
-B ADAPTER 5'/3 adapter to be removed from second read in a pair.
-U LENGTH Remove LENGTH bases from second read in a pair.
-p FILE, --paired-output FILE
Write second read in a pair to FILE.
--pair-adapters Treat adapters given with -a/-A etc. as pairs. Either both
or none are removed from each read pair.
--pair-filter (any|both|first)
Which of the reads in a paired-end read have to match the
filtering criterion in order for the pair to be filtered.
Default: any
--interleaved Read and/or write interleaved paired-end reads.
--untrimmed-paired-output FILE
Write second read in a pair to this FILE when no adapter
was found. Use with --untrimmed-output. Default: output to
same file as trimmed reads
--too-short-paired-output FILE
Write second read in a pair to this file if pair is too
short.
--too-long-paired-output FILE
Write second read in a pair to this file if pair is too
long.
(rnaseq) root 12:06:01 ~
就是一个简单的perl wrapper，打包了fastqc和cutadapt，但是却非常实用。
因为cutadapt的参数选择实在是有够复杂，光接头类型就有5种，还有各种参数，大哥，我就想去去接头、trim一下质量而已，你就不能自动搞了吗。不要给选择困难症的我这么多选择啊。
想自动化？trim_galore 完美的符合了你的需求，无需自己去查接头，全自动质量过滤，噢耶。
还能和mutilqc完美对接，生成网页版报告。
使用比较简单直接：
其他参数无需选择，默认的就可以了，是不是十分之自动化。
参见说明文档