Hi,
I've been using bowtie function on Galaxy. I just have a quick question with regards to setting seed length when mapping.
I've trimmed my sequencing reads to let say 25bp because of poor read quality. The default mapping parameter state seed length is 28bp.
Would this affect the mapping result?
Will the mapping even be valid taking more than the sequence reads a seed?
Is it better to reduce seed length to something like 20bp?
Many thanks for your help
I've been using bowtie function on Galaxy. I just have a quick question with regards to setting seed length when mapping.
I've trimmed my sequencing reads to let say 25bp because of poor read quality. The default mapping parameter state seed length is 28bp.
Would this affect the mapping result?
Will the mapping even be valid taking more than the sequence reads a seed?
Is it better to reduce seed length to something like 20bp?
Many thanks for your help
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