Hi Team,
Loving Galaxy! When I run my data, I use the same protocol for most all datasets. However, after running the alignment tool (usually Bowtie2 or HISAT), I am unable to get past the next analysis of using Cufflinks. I have tried it both with and without the gff file for reference annotation. Cufflinks remains in que and won't run. This has been happening for a while now. Is this expected from time to time? Also, if Cufflinks does run using the reference genome gaff file, I don't get FPKM values (when using the reference annotation gff file) but I will get an abbreviated gene symbol instead of a Cuff ID. All FPKM values show as zero. When I use Cufflinks without the reference annotation gff file, I don't get a gene symbol abbreviation, but I do get FPKM values. How can I use Galaxy tools to merge both the Cufflinks sets so that the files align both FPKM values and gene abbreviations together and match? The start/end loci should match, so that the gene symbols and FPKM values correlate to each other...
Thanks!
This is a known issue our team is actively working to correct. The inputs are not a factor - job dispatch had an issue. The advice is to allow queued jobs to remain queued. These will execute once the issue is resolved. More feedback after the fix, to let you and others having the same issue know what is going on.
For the data issue and reference annotation, there is probably a genome mismatch problem. Make sure that the ref genome used for alignments and the ref annotation used with tools are from the same exact genome build (compare the chromosome identifiers in the BAM datasets versus the GTF file).
Thanks! Jen, Galaxy team