fastq to fasta conversion

kwtennis311 · 06-10-2010, 12:39 PM

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 · 06-10-2010, 01:06 PM

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 · 06-10-2010, 01:55 PM

Quote:

Originally Posted by Bio.X2Y

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 · 06-10-2010, 02:30 PM

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 · 06-11-2010, 12:06 PM

thanks guys, Biopython did the trick

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06-10-2010, 12:39 PM	#1
kwtennis311 Junior Member Location: Earth Join Date: Jun 2010 Posts: 7	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

06-11-2010, 12:06 PM	#5
kwtennis311 Junior Member Location: Earth Join Date: Jun 2010 Posts: 7	thanks thanks guys, Biopython did the trick

06-10-2010, 01:06 PM	#2
Bio.X2Y Member Location: Europe Join Date: Apr 2010 Posts: 46	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.

06-10-2010, 02:30 PM	#4
Bio.X2Y Member Location: Europe Join Date: Apr 2010 Posts: 46	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.