Hi, I'm attempting RNA-seq data analysis on *Vibrio cholerae* samples, at galaxy main https://main.g2.bx.psu.edu/. I was able to align transcripts using Ion Torrent's TMAP aligner. I uploaded the BAM files and used the cufflinks tool, which gave me FPKM scores for various transcripts. Now I want to extract the relevant gene_id for each mapped transcript using a reference genome. I tried using CuffCompare for this purpose using a reference file from the UCSC archaea database or using a FASTA file from history. In either case, cuffcompare gives me an error. Error1: (When using a reference genome from the UCSC archaea database) An error occurred running this job:*cuffcompare v2.0.2 (3522) No sequence data found for dbkey vibrChol1, so sequence data cannot be used. cp: cannot stat `/galaxy/main_pool/pool4/tmp/job_working_directory/004/846/4846005/cc_output.input1.refmap': No such file or directory cp: cannot stat `* * * Error 2: (When using a reference genome from history) An error occurred running this job:*cuffcompare v2.0.2 (3522) cuffcompare -o cc_output -r /galaxy/main_pool/pool1/files/005/515/dataset_5515739.dat -s ref.fa ./input1 Error running cuffcompare. You are using Cufflinks v2.0.2, which is the most recent release. No fasta index found for ref* * * Could you help me figure out what's going on? Thanks, -Samit Regards, Samit Watve Graduate Teaching Assistant, School of Biology, Georgia Institute of Technology PhD Student at the Hammer Lab, Office: Cherry Emerson, 218-E, 310 Ferst Drive Atlanta GA School of Biology, Georgia Institute of Technology Lab Page: http://www.hammerlab.biology.gatech.edu/