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Old 07-28-2010, 02:08 AM   #1
Location: Sweden

Join Date: Nov 2009
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Default Interleaved mate pair fastq after quality filtering

I am looking for a script that can produce an interleaved fastq file and a file of orphaned [single end] reads from two input fastq files. The two read pairs have been quality filtered using fastx-toolkit 'fastq_quality_filter', which breaks the exact pairing that previously existed.

Has anyone come across a script to do this rather than just to interleave two perfectly paired sets of fastq files?
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Old 08-10-2010, 04:19 AM   #2
Peter (Biopython etc)
Location: Dundee, Scotland, UK

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There are some replies on the cross-post,
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