I am new to Galaxy, but based on my understanding of how things work, I mapped some RNA-seq data from E. coli K-12 onto a reference genome obtained via UCSC using Bowtie, and then ran that through HTSeq to get a count of reads for the different genes. All of that worked well, but what was missing from the reads corresponding to RNA genes, such as rRNA, tRNA and regulatory RNAs. Is there a way to perform the analysis and get counts for RNA genes as well? This is critical for our analysis, as most of the hits we are expecting from our experiment should correspond to RNA genes.
Also it was not clear which version of the E. coli genome sequence I have downloaded from the UCSC site. There are many K-12 genomes available now, and I'd like to be sure that the version I am using corresponds to the strain we are using (which is actually the first K-12 genome to be sequenced). Is there any way to get information on the K-12 genome (e.g., Genbank or Refseq ID) that is available on the UCSC site?
Other than that, I am really pleased with Galaxy because it has given beginners such as myself the power to manipulate HTS data. Keep the good work going.
Chaitanya Jain Associate Professor, University of Miami