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Old 10-27-2010, 05:56 PM   #1
juan
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Location: New York City

Join Date: Aug 2009
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Red face Paired end reads: line # does not match

Hello,
I have a GAII paired-end run (seven lanes, run1 and run2 for each lane are the forward and reverse ends of a pair).

For 3 of the lanes, very few of the reads mapped successfully (< 20%). I just realized that the line # is different in the run1 and run2 of these lanes. The last read in both files is a pair (same QNAME), but there appears to be extra reads in run2.

Has someone else experienced this problem, can it be caused by changes in the Illumina Pipeline settings? If the reads are out of order, does BWA and Bowtie check the read QNAME for mismatches?

If not, has someone else already written a high-speed tool for checking and removing the extra reads from huge FASTQ files?

Thanks
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bwa 0.5, fastq, illumina sequencing, paired-end

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