1:在安裝該軟件時候遇到，尤其時運行;make命令時候報錯：“fgets called with bigger size thanlength of destinationbuffer”，請安裝比較新版本，就解決了該問題。其它的基本上就按照網站上的說明一步一步做就可以了。（我用的是Ubuntu）
2:如果在運行fastx_quality_stats過程中出現“fastx_quality_stats: Invalid quality score value (char '#'ord 35 quality value -29) on line 4”，請在參數中加入“-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.(格式轉換)
Usage: fastq_to_fasta–i input.fastq –o out.fasta
-v: report number of sequences
2-2 FASTQ Information:Chart Quality Statistics and NucleotideDistribution（基本統計）
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 截取的起始位點
-l 截取的結束位點
-i 輸入的文件可以是fasta,也可以使fastq
2-5：FASTQ/AClipper：Removing sequencing adapters /linkers(刪除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（刪除重複序列，找到獨一序列）
Usage: fastx_collapser -v -i BC54.trimmed.fa -oBC54.collapsed.fa
2-7: FASTQ Quality Filter: Filterssequences based on quality(質量控制)
Usage: fastq_quality_filter -iBC54.trimmed.fa -o BC54.collapsed.fa –q N –p N
-q Minimum quality score ofbase
-p 大於最小鹼基質量[q值]所佔的100%