Hi, I realize that many users have posted similar questions and the galaxy team has diligently addressed dozens of similar queries. After reading whatever I could find on the subject, I am still in the dark on how to fix my annotation file, assuming that's what causes cufflinks to return FPKM of zero on all the rows. I understand that genome file and annotation file have to be matched, i.e., using the same chromosome designation. I'm copying here the first lines of the genome file (from the pig, Sus scrofa), the first row of the annotation file below, and below that the first rows of the TopHat BAM file converted to SAM.
Genome FASTA file:
susScr3_gold_GL878569.2 range=chr1:1-174389 5'pad=0 3'pad=0 strand=+ repeatMasking=none AATCGACGCCACACGCAGGCCAGTTCCGAGCTGCATCTGGGACCTGCTCC ...
GTF annotation file: chr1 susScr3_refGene start_codon 133903981 133903983 0.000000 + . gene_id "NM_214429"; transcript_id "NM_214429"; ...
TopHat SAM file: D00780:57:C8BGWANXX:8:1305:3315:34658 0 susScr3_gold_AEMK01000005.1 1 255 101M * 0 0 GGGAGCAGCAGCTGCTTCTACAGTTTGTTTTGAAATGGCGTTAGATAAAATAAGGGAATAAATAGAGGGGGTAAGAGGCAGACTCTCCATCCCCGTGTCAC BBBBBFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFBFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF NM:i:0 NH:i:1
The question I have is how do I make FASTA and GTF files compatible (assuming that's the issue)? Do I replace "chr1" with "susScr3_gold_GL878569.2 range=chr1"?
BTW, I ran into a similar problem regardless if I download genome and annotation from UCSC or iGenomes.
Finally, I saw that the usegalaxy.org has the built-in pig genome, but cufflinks doesn't seem to see a cached matching annotation file, hence I used one in my history. Is it possible to install the Sus scrofa annotation file?