I'm trying to reproduce the results from a dataset from RNAseq I found on GEO. After I processed with the standard options on everything the FPKM values are a little higher. I noticed that in cufflinks I have different values, in their output file they have this command line:
cufflinks --library-type fr-firststrand --no-effective-length-correction --min-isoform-fraction 0 --pre-mrna-fraction 0.05 --junc-alpha 0.05 --max-bundle-length 5500000 -b
I'm not sure how to translate that into cufflinks in Galaxy.
Thanks a lot.