thanks
thanks guys, Biopython did the trick
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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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Originally posted by Bio.X2Y View PostHowever, I don't think it makes any sense to create a fasta file "containing the quality scores". Fasta files are used to represent sequences.
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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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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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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