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Help in cufflinks -- all the FPKM values are 0

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!

next-gen rna-seq
• 3,551 views • link
updated by Ram Ram • written by caelyn5201314 • caelyn5201314

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.

• 0 views • link
updated by Ram Ram • written by Vishaka Datta • Vishaka Datta

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

• 0 views • link
updated by Ram Ram • written by caelyn5201314 • caelyn5201314

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

• 0 views • link
updated by Ram Ram • written by Phil S. Phil S.

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";
• 0 views • link
updated by Ram Ram • written by caelyn5201314 • caelyn5201314

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