I am using the cufflinks RNA-seq tool. It is of great help to my project. And I have some questions about the tool.
When I run the cuffcompare on my mac, sometimes it won't generate .combined.gtf file and .tracking file but generate an .loci file.
I don't why. The dataset is from GEO. It's accession number is GSE11892.
My codes are as follows:
./cufflinks B.sam.sorted
./cuffcompare -r Homo_sapiens.GRCh37.57.gtf transcripts.gtf
B.sam.sorted is the .sam file that sorted from the sam output of bowtie.
Homo_sapiens.GRCh37.57.gtf is downloaded from Ensembl.
When I run the cuffcompare on my mac, sometimes it won't generate .combined.gtf file and .tracking file but generate an .loci file.
I don't why. The dataset is from GEO. It's accession number is GSE11892.
My codes are as follows:
./cufflinks B.sam.sorted
./cuffcompare -r Homo_sapiens.GRCh37.57.gtf transcripts.gtf
B.sam.sorted is the .sam file that sorted from the sam output of bowtie.
Homo_sapiens.GRCh37.57.gtf is downloaded from Ensembl.