fastq 文件介绍

name

NT064_S43_L001_R1_001.fastq.gz

第一部分：样本名
第二部分：（和 illumina Experiment Manage 的编号一致）S1 .. S* 后面跟的数字与样本在Sample Sheet中的顺序一致，从1开始。不能分配到确定样本的read会归到S0（Undetermined_S0）
第三部分：泳道lane的编号
第四部分：R1表示read1，R2表示read2。R1和R2为paired end reads
第五部分：通常为001

查看fastq的文件格式

[xmxjy@xmxjy filter]$ less allhpv.fastq.gz | head
@TPNB500301:48:HHTKNAFXY:1:11101:11715:1039 1:N:0:TCCGGAGA+NGGATAGG
TGACGNTCTCAATATATGTGTGCTTTTTTGCATATTCATAATCTCCCTACTTTATTTTCTTTTATTTTTAATTGATACATAATCATTATACATATTTATGGGTTAAAGTGTAATGTTTTAATATGTGTAAACATATTGACCAAATCAGGGT
+
AA6AA#EEEEE6EEEEEEEEEEEEE6EEEAEEEAAEEEA/E6/EE/EE6EAAEAEEE6EAEEE6EEEEE/EEEEEAEE/EEEEEEAAEAEEEAEE<EEEE/EEAAE/EEEEEEE/EEEEAEEEEEEEEE/AEAEEAEE<<A/EE<<E//EE
@TPNB500301:48:HHTKNAFXY:1:11101:14066:1039 1:N:0:TCCGGAGA+NGGATAGG
AGACTNTCGTAATATATGTGTGCTTATTTGCATATTCATAATCTCCCTACTTTATTTTCTTTTATTTTTAATTGATACATAATCATTATACATATTTATGGGTTAAAGTGTAATGTTTTAATATGTGTACACATATTGACCAAATCAGGGT
+
6AAAA#EEEEEEEEEEEEAAEE/E/EEEEEAEE6EAA/EAEEEE</EEEA/EEEEEEEEEE6EEEE/E/EAEEAE/EAAEE6EEEEEEEAEEAEEEEEEEEEAEEAEAEEE/EEAEEEE/EEA/EEEE/EE<EAE/E/<E<E/EA<EAAEE

意思如下：
Each entry in a FASTQ file consists of four lines:
• Sequence identifier
• Sequence
• Quality score identifier line (consisting of a +)
• Quality score

@TPNB500301:48:HHTKNAFXY:1:11101:11715:1039 1:N:0:TCCGGAGA+NGGATAGG

以：分隔
@<instrument>
<run number>
<flowcell ID>
<lane>
<tile>
<x-pos>
<y-pos>
<read>
<is filtered>
<control number>
<index sequence>

下面是别人的一张图片

image.png

Quality score

The character '!' represents the lowest quality while '~' is the highest. Here are the quality value characters in left-to-right increasing order of quality (ASCII):

!"#$%&'()*+,-./0123456789:;<=>?@ABCDEFGHIJKLMNOPQRSTUVWXYZ[\]^_`abcdefghijklmnopqrstuvwxyz{|}~

image.png

Q值

质量值Q是p的整数映射（即相应碱基判定不正确的概率），主要有两种不同的公式被使用。第一种是评估碱基判定的可靠性的不标准Sanger变体，也称为Phred质量分数：

Solexa流程（即与Illumina Genome Analyzer一起交付的软件）较早使用了不同的映射编码概率p/（1-p），而不是p：

测序质量值和准确度

Phead Quality Score	Probability of incorrect base call	Base call accuracy
10	1 in 10	90%
20	1 in 100	99%
30	1 in 1000	99.9%
40	1 in 10000	99.99%
50	1 in 100000	99.999%

维基百科
https://en.wikipedia.org/wiki/FASTQ_format#File_extension
中文翻译
http://www.cnblogs.com/yahengwang/p/8973948.html
shell 操作
https://www.jianshu.com/p/bc1fe435879c