fastq and fasta

通常fastq序列文件用四行描述一个序列

• Line 1 begins with a '@' character and is followed by a sequence identifier and an optional description.
• Line 2 is the raw sequence letters.
• Line 3 begins with a '+' character and is optionally followed by the same sequence identifier.
• Line 4 encodes the quality values for the sequence in Line 2, and must contain the same number of symbols as letters in the sequence.The character '!' represents the lowest quality while '~' is the highest.
• fastq转化为fasta （可以用fastx-tools），但是通常一个awk命令解决，多好！例如：
• awk 'NR%4==1{printf ">%s\n", substr($0,2)}NR%4==2{print}' > output_file.fa 
• 也可以上游处理之后，管道一下，交给下游
• zcat input_file.fastq.gz 或者 gzip -d input_file.*.gz | awk 'NR%4==1{printf ">%s\n", substr($0,2)}NR%4==2{print}' > output_file.fa