FASTQ format

FASTQ format

每个FASTQ文件中每个序列通常有四行信息：

1： 以 '@' 字符开头，后面紧接着的是序列标识符和可选字段的描述(类似FASTA title line).

2： 序列

3： 以 '+' 字符开头， 后面紧接着的是可选字段的描述性信息

4： 第二行序列的质量信息

Illumina sequence identifiers

@HWUSI-EAS100R:6:73:941:1973#0/1

sequence identifiers	description
HWUSI-EAS100R	the unique instrument name
6	flowcell lane
73	tile number within the flowcell lane
941	'x'-coordinate of the cluster within the tile
1973	'y'-coordinate of the cluster within the tile
#0	index number for a multiplexed sample (0 for no indexing)
/1	the member of a pair, /1 or /2 (paired-end or mate-pair reads only)

Versions of the Illumina pipeline since 1.4 appear to use #NNNNNN instead of #0 for the multiplex ID, where NNNNNN is the sequence of the multiplex tag.

With Casava 1.8 the format of the '@' line has changed:

@EAS139:136:FC706VJ:2:2104:15343:197393 1:Y:18:ATCACG

sequence identifiers	description
EAS139	the unique instrument name
136	the run id
FC706VJ	the flowcell id
2	flowcell lane
2104	tile number within the flowcell lane
15343	'x'-coordinate of the cluster within the tile
197393	'y'-coordinate of the cluster within the tile
1	the member of a pair, 1 or 2 (paired-end or mate-pair reads only)
Y	Y if the read is filtered, N otherwise
18	0 when none of the control bits are on, otherwise it is an even number(偶数)
ATCACG	index sequence

将FASTQ 转换为 FASTA 格式:

zcat input_file.fastq.gz | awk 'NR%4==1{printf ">%s\n", substr($0,2)}NR%4==2{print}' > output_file.fa

#printf 命令的语法：format-string 为格式控制字符串，arguments 为参数列表。
printf  format-string  [arguments...]

#substr(s,p) 返回字符串s中从p开始的后缀部分
#substr(s,p,n) 返回字符串s中从p开始长度为n的后缀部分。