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?

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