fastq to fasta conversion

[kwtennis311]

How can I convert my fastq files to two fasta files with one containing the reads and another containing the quality scores?

Thanks

[Bio.X2Y]

You could use awk to create a simple fasta file from your fastq, e.g.

awk 'NR % 4 == 1 {print ">" $0 } NR % 4 == 2 {print $0}' my.fastq > my.fasta

However, I don't think it makes any sense to create a fasta file "containing the quality scores". Fasta files are used to represent sequences.

[sklages]

However, I don't think it makes any sense to create a fasta file "containing the quality scores". Fasta files are used to represent sequences.

... and their corresponding qualities ..

mySeq.fasta :
>mySeq
ACGTACGT

mySeq.fasta.qual:
>mySeq
22 22 33 33 22 22 33 44

There are still some programs which need to be fed with fasta/qual :-)

Anyway, qualities need to be converted to phred-stye ..

[Bio.X2Y]

Thanks sklages! I wasn't aware of qual files.

kwtennis311, there seem to be some existing posts on this, you might find answers in this, e.g. http://seqanswers.com/forums/showthread.php?t=3730.

[kwtennis311]

thanks

thanks guys, Biopython did the trick