cufflinks run with STAR output gives 0 FPKM

[pm2016]

Hi 

I am running cufflinks on alignment files produced from STAR. However, I seem to get 0 FPKM for all my genes and transcripts. I am using version 2.5.2a version of STAR and 2.2.1 version of cufflinks.

Here are the commands that I use:

cufflinks -o sample1-cufflinks -p 12 -G ~/Homo_sapiens/Ensembl/GRCh37/Annotation/Genes/genes.gtf -b ~Homo_sapiens/Ensembl/GRCh37/Sequence/WholeGenomeFasta/genome.fa -u -L sample1 sample1.bam

~/bin/STAR-2.5.2a/bin/Linux_x86_64/STAR --runThreadN 8 --runMode alignReads --genomeDir ~/Homo_sapiens/Ensembl/GRCh37/Sequence/STARIndex --outFileNamePrefix sample1 --outSAMstrandField intronMotif --outFilterIntronMotifs RemoveNoncanonical --outFilterMatchNmin 20 --outSAMtype BAM SortedByCoordinate --outReadsUnmapped Fastx --outWigType wiggle --readFilesIn sample1.1.fastq sample1.2.fastq

Any help would be greatly appreciated.

Thanks

Prakriti

[Alexander Dobin]

Hi Prakriti,

your commands look OK, not sure what is going on. Could you please cut out ~100,000 reads and send them as a BAM file?

Cheers

Alex