FASTX-Toolkit 使用说明

警告：
1:在安装该软件时候遇到，尤其时运行;make命令时候报错：“fgets called with bigger size thanlength of destinationbuffer”，请安装比较新版本，就解决了该问题。其它的基本上就按照网站上的说明一步一步做就可以了。（我用的是Ubuntu）
2:如果在运行 fastx_quality_stats过程中出现“fastx_quality_stats: Invalid quality score value (char '#'ord 35 quality value -29) on line 4”，请在参数中加入“-Q33”,例如： fastx_quality_stats -ifastq_file -Q 33 -o fq_stat

 

1：The FASTX-Toolkit is acollection of command line tools for Short-Reads FASTA/FASTQ filespreprocessing.

2：Available Tools

2-1  FASTQ-to-FASTAconverter：Convert FASTQ files to FASTAfiles.(格式转换)

Usage: fastq_to_fasta–i     input.fastq –o out.fasta

-v: report number of sequences

2-2  FASTQ Information:Chart Quality Statistics and NucleotideDistribution（基本统计）

      Usage: fastx_quality_stats–i      input.fastq -o out.txt

          fastq_quality_boxplot_graph.sh –i out.txt –o out_quality.png -t "MyLibrary"

 

fastx_nucleotide_distribution_graph.sh -iout.txt -o out_nuc.png -t "MyLibrary"

-t :Title (usually the solexa file name) - will be plotted onthe graph

 

 

2-3  FASTQ/A Barcodesplitter: Splitting a FASTQ/FASTA files containing multiplesamples（解Barcode序列）

Usage：cat s_2_100.txt |/usr/local/bin/fastx_barcode_splitter.pl --bcfile mybarcodes.txt --bol --mismatches 2 --prefix/tmp/bla_ --suffix ".txt"

Input：s_2_100.txt

Barcode file: mybarcodes.txt

 

 

--bol: Try to match barcodes at the BEGINNING ofsequences.

--eol: Try to match barcodes at the END ofsequences.

--mismatches: Max number of mismatches allowed.Default is 1

--exact: Same as '--mismatches 0'

--prefix: File prefix

--suffix: File suffix

2-4:fastx_trimmer（截取序列）

      Usage：fastx_trimmer -v -f 1 -l 27 -i BC54.clipped.fa -oBC54.trimmed.fa

      -f 截取的起始位点

      -l 截取的结束位点

      -i 输入的文件可以是fasta,也可以使fastq

 

2-5：FASTQ/AClipper：Removing sequencing adapters /linkers(删除Adapter序列)

 

Usage: fastx_clipper -v -i BC54.fa -aCTGTAGGCACCATCAATTCGTA -o BC54.clipped.fa

-a: Adapter sequence, default is CCTTAAGG

 

2-6: FASTQ/ACollapser（删除重复序列，找到独一序列）

Usage: fastx_collapser -v -i BC54.trimmed.fa -oBC54.collapsed.fa

 2-7: FASTQ Quality Filter: Filterssequences based on quality(质量控制)

 

Usage: fastq_quality_filter -iBC54.trimmed.fa -o BC54.collapsed.fa –q N –p N

-q Minimum quality score ofbase

-p 大于最小碱基质量[q值]所占的100%