Hi There

Im trying to map RNA-seq data to a reference genome in Galaxy (Main instance) using both Bowtie 1 and Bowtie 2. Im currently using publicly available data (http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE28755) which is not available in FASTQ format - only the raw sequences with the read count. Is there a way to set the input data for bowtie to raw, as is possible using the terminal? Or is there a way to convert a raw sequence to FASTQ (not sure if this would work, but it might be possible if I assigned accession numbers to each sequence and made all the quality scores identical)?

Thanks very much
Jonathan Glass
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