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 
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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