Hi, I hoped that someone could shed some light onto this . I am attempting to map a set of 2x 150 illumina PE data from a DNA resequencing project. The run had an issue where the quality of the last 50 or so reads of the second run tail off quite considerably. I thought to trim the second read such that the poorer sequence bases are stripped form the end of the read. I attempted to do this using the FASTQ quality trimmer then mapping both reads using bowtie. When I did this however, I went from an alignment of 34% passing filter reads aligned not trimmed (which is not good to start off with), to 0.18%. trim command was set as defaults: Any ideas what I could be doing wrong? ******************************************************************************************************************** This message may contain confidential information. If you are not the intended recipient please inform the sender that you have received the message in error before deleting it. Please do not disclose, copy or distribute information in this e-mail or take any action in reliance on its contents: to do so is strictly prohibited and may be unlawful. Thank you for your co-operation. NHSmail is the secure email and directory service available for all NHS staff in England and Scotland NHSmail is approved for exchanging patient data and other sensitive information with NHSmail and GSi recipients NHSmail provides an email address for your career in the NHS and can be accessed anywhere For more information and to find out how you can switch, visit www.connectingforhealth.nhs.uk/nhsmail ********************************************************************************************************************