When using bowtie on Galaxy you can choose to use the 'full parameter' list. This will provide you with additional parameters among them are the ability to trim from either or both the 3' and 5' end of your reads. Not trimming would end up greatly decreasing the number of sequences you will align.
There are also programs available were you can 'clip-off' adaptor sequences from the fastq file.
There are also programs available were you can 'clip-off' adaptor sequences from the fastq file.
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