Question: Cufflink Does Not Work!
0
Jennifer Hillman Jackson ♦ 25k wrote:
Hello Di Nguyen,
Without seeing your history, my initial guess is that the SAM output
from the mapping runs need to be sorted before running Cufflinks.
(Tophat, which is designed to map spliced RNA-seq data, sorts the SAM
output as part of the data processing, but BWA and Bowtie do not).
The workflow provided on this FAQ can be followed to sort SAM files
for
Cufflinks:
https://main.g2.bx.psu.edu/u/jeremy/p/transcriptome-analysis-
faq#faq2
If you continue to have problems, please submit a bug report (click on
"green bug" icon from the error Cufflinks dataset as run on the main
public Galaxy instance (http://usegalaxy.org), leave all inputs and
the
error dataset undeleted, note this email address in the comments if it
differs from your Galaxy account email address (so that I can link the
two issues together), and we can provide more feedback.
http://wiki.g2.bx.psu.edu/Support#Error_from_tools
Hopefully this helps,
Jen
Galaxy team
--
Jennifer Jackson
http://galaxyproject.org