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Old 09-08-2014, 01:37 PM   #32
Brian Bushnell
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Location: Walnut Creek, CA

Join Date: Jan 2014
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If you are sure those files go together, then the most likely problem is that you used a different program upstream that was not pair-aware and removed some reads from one file but not the other. The best thing to do is redo the processing on the original files with something that retains pairing. Failing that, you can attempt to fix them like this:

cat clean_1g_C10_R2.fastq.gz tc_clean_1g_C10_R2.fastq.gz | repair.sh -Xmx4g in=stdin.fq.gz out1=r1.fq.gz out2=r2.fq.gz outs=singletons.fq

...which will redo the pairings based on the read names. It may help if you could print the first and last 4 lines of each file, as well as the word counts, and/or explain exactly what processing steps were done on the reads prior to quality-trimming.
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