No, the /1 still goes at the end, theres just no space. Do you have any concept of what a properly formed fastq file is meant to look like? Try this head GAMMA-1.solexa.fastq @D61655M1:276:D10YJACXX:8:1101:1456:1955/1 NCTGNAGTGTNNGATNCGGGGTTNNNNNNNNNNACNTTNNNNNNNNNNGNNNGNNNTTGAANNNNNNNNTNACNGTNTNATNAANNNNTTCGGACNACAT + #0;@#2@=@?##32@#2=>@@<@#############################################################################