Convert paired end fastq file to fasta format
Merge reads1 and read2 by using shuffleSequences_fastq.pl script:
perl shuffleSequences_fastq.pl Read1.fastq Read2.fastq ReadsMerge.fastq
Now how to convert paired end fastq file into fasta format correctly?
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Answer from HengLi: A: Fastq Convert To Fasta
As much as I dislike the absence of reformat.sh from the solutions, I agree that this is a good answer.