Limiting Illumina Paired-End Reads

[cryptic_star]

I'm in the process of testing some various sequencing techniques with reads of various lengths. I have one data set I would particularly like to use because of its read length, but it is a paired end read; I am only testing on non-paired end reads. Would it be valid for me to remove the /1 or /2 from the ends of the id sequence (FASTQ Illumina formatting) and then run all the lanes through? Or should I only run half of every lane through (for example, all the 1 halves of the pairs? Or is even trying to do this misrepresenting the data?

Thanks.

[krobison]

I would just use one orientation; the paired end nature of the sets means the distribution of reads on the target genome/transcription is more concentrated than two separate runs.