I have Illumina HiSeq2000 paired end reads from RNA sequencing (CASAVA version 1.8). I have gotten the information that the FastQ file quality encoding is in Sanger format. They have been quality checked and screened.
Now my question is, do they need any kind of grooming before mapping them to a reference genome? I'm thinking of Fastq grooming in Galaxy. Or is it fine to upload them as fastqsanger and assemble them straight away using Tophat?