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
Usage: fastq_to_fasta–i
-v: report number of sequences
2-2
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
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)
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
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%