4.5 years ago by
Keep in mind that when you collapse sequences, the original quality score is going to be lost. There isn't a way to merge the quality scores and they probably differ between the reads, even if the sequence is the same. Still - if you want to do this, convert to fasta, collapse, then convert back to fastq with default quality scores assigned, using the tool "NGS: QC and manipulation -> Combine FASTA and QUAL".
Your question does not seem to fit the tags assigned - you can change them or I can. Bowtie/Bowie2 would not be a good choice for mapping RNA-seq reads to yeast because of the splicing (Tophat/Tophat2 is better). Also, removing redundancy in reads will almost certainly bias the expression profile of the data, also not a good idea for RNA-seq. If really doing RNA-seq, I wonder what tutorial are you following .. here are some others to explore: https://wiki.galaxyproject.org/Support#Tools_on_the_Main_server:_RNA-seq
Best, Jen, Galaxy team