Question: Help in cufflinks -- all the FPKM values are 0
0
gravatar for caelyn5201314
4.7 years ago by
China/Beijing/Chinese Academic Of Science
caelyn520131410 wrote:

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 !!!

rna-seq next-gen • 1.8k views
ADD COMMENTlink written 4.7 years ago by caelyn520131410

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.

ADD REPLYlink written 4.7 years ago by Vishaka Datta80

The annotation file is correct...if i use -g then nothing wrong 

ADD REPLYlink written 4.7 years ago by caelyn520131410

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

ADD REPLYlink written 4.7 years ago by Phil S.660

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";

ADD REPLYlink written 4.7 years ago by caelyn520131410
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 766 users visited in the last hour