Run flash on the two fastq's, a la:
flash Ustilago-5_S9_L001_R1_001.fastq Ustilago-5_S9_L001_R2_001.fastq
This generates "out.extendedFrags.fastq" of the stitched reads.
Then run revcomp_fastq on the result - this script will correct the orientation of reads and trim the 454 emPCR primer sequences, giving you two files ready for qiime as described here.
./revcomp_fastq out.extendedFrags.fastq > seqs.fq 2> bc.fq
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