I have Illumina sequences from a cDNA sample. I want to map the reads to a reference genome and calculate expression levels. I think I will map using bowtie/tophat.
The adaptors are removed from my sequences, but I wonder whether I need to trim away the low quality bases at the 3'-end of the reads? Or is this taken into account in the mapping?
Thanks!
The adaptors are removed from my sequences, but I wonder whether I need to trim away the low quality bases at the 3'-end of the reads? Or is this taken into account in the mapping?
Thanks!
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