Question: Error Running Cuffcompare On Galaxy Server
0
Samit Watve • 10 wrote:
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/