OK, I can understand what you're doing here but if your $FILE represents "read_1 read_2" then your output BAM file will be called "read_1 read_2".bam which is going to cause some problems for you. Note that novoalign only recognizes paired-end reads from them being in separate files so you cannot concatenate them and assume it's going to pair them together.
Originally posted by nguyendofx
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