Truncating reads in fastq file

[timydaley]

I want to simulate shorter reads from a particular dataset. Say I want 50bp paired end reads from a 100bp paired end read data set while keeping the same insert size. Would I take the first 50 characters of the sequence and the score strings from each end? Or would I take the first 50 from the first end and the last 50 from the last end.

Extracting the characters is easy with a simple awk command. I'm just curious about the order.

Thank you very much.

[mastal]

the first 50 from the second reads of the pair, if you want to keep the same insert size, because the sequences are given from 5' to 3', so the first 50 bases are the ones from the end of the fragment.