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Old 09-09-2010, 11:50 PM   #1
sandhya
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Location: India

Join Date: Sep 2010
Posts: 11
Default Fastq format and Paired-end reads

Dear all,

I have recently started work on sequenced data. We have paired-end reads from Illumina in Fastq format and I had some questions about these.

1. In the fastq format, what do the numbers in the 1st line mean?
@0:1:1:34:429
GAAGNAAAAATAAAAGCATTAGNAGAAATTTGTACA
+
IIII$IIIII&IIIIIIIIIII$IIIIIIIIIIIII

2. I see that these numbers (or 1st lines) always have a one-to-one mapping between the 2 paired datasets (ie for left and right reads). Therefore is it right to say that the 1st entry in dataset1 (of left reads) is paired with the 1st entry in dataset2 (of right reads) and likewise?

Please advice.
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