I have DNA sequencing data (targeted sequencing) produced by MiSeq. The size of the insert is 250bp, it was sequenced by using paired end reads and the reads are overlapping. I am planning to use velvet on Galaxy to perform de novo assembly. As I understand, velvet requires the input to be in one file, so the paired end reads must be joined prior to the assembly.
I've been trying to use fastq-join tool in Galaxy; however, it keeps giving error messages, saying that the ids in one file cannot be found in the other file.
I was wondering what should I do to make the fastq-join tool to run successfully? Does it need all the reads to be sorted in both files and does it need only the reads that appear in both files?
If so, how could I perform these operations in Galaxy?
Thank you very much for the help!