Help in cufflinks -- all the FPKM values are 0

Question

[caelyn5201314]

Hi,all!

I use the cufflinks with the parameter -G and found that all the FPKM values are 0.

This is my command:

/share_bio/nas2/zhangz_group/xial/software/cufflinks-2.2.1.Linux_x86_64/cufflinks \
  -o /share_bio/nas2/zhangz_group/xial/test/$Filename2[$i]/$realFiles[$j]/cufflinks_result \
  -p 8 \
  -G /share_bio/nas2/zhangz_group/xial/cufflinks_anno/allcomB.combined.gtf \
  /share_bio/nas2/zhangz_group/xial/data-tophat/$Filename2[$i]/$realFiles[$j]/$tophatResult[$k]

Thanks all!

[Vishaka Datta]

The command you've used looks quite complicated. Are you sure the correct genome annotation file is being passed to cufflinks? Check the value of all the shell variables used to see if it's the correct file being opened.

[caelyn5201314]

The annotation file is correct. If I use -g then nothing wrong

[Phil S.]

Have you checked that chromosome names are identical in annotation and genome reference?

[caelyn5201314]

Yes, this is my annotation file

Chr1    irgsp1_rep    exon    2983    3268    .    +    .    gene_id "XLOC_000001"; transcript_id "TCONS_00000001"; exon_number "1"; gene_name "Os01g0100100"; oId "Os01t0100100-01"; tss_id "TSS1";
Chr1    irgsp1_rep    exon    3354    3616    .    +    .    gene_id "XLOC_000001"; transcript_id "TCONS_00000001"; exon_number "2"; gene_name "Os01g0100100"; oId "Os01t0100100-01"; tss_id "TSS1";