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Old 06-10-2010, 11:39 AM   #1
kwtennis311
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Question fastq to fasta conversion

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

Thanks
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Old 06-10-2010, 12:06 PM   #2
Bio.X2Y
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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.
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Old 06-10-2010, 12:55 PM   #3
sklages
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Quote:
Originally Posted by Bio.X2Y View Post
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 ..
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Old 06-10-2010, 01:30 PM   #4
Bio.X2Y
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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.
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Old 06-11-2010, 11:06 AM   #5
kwtennis311
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Thumbs up thanks

thanks guys, Biopython did the trick
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