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
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?



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/
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