cufflinks output against annotation file

[masylichu]

hello, everyone,

i run the cufflinks to calculate the RPKM(or FPKM) for annotated genes for C.elegans.

i type in the command.

cufflinks -p 8 -G WormBase190/ce6_sangerRNA.gtf N2.sort.bam

the version of cufflinks is the latest, cufflinks-1.1.0.

however, the output is like this.

chrI    Cufflinks   transcript  1738651 1738674 1   +   .   gene_id "Y71G12B.29"; transcript_id "Y71G12B.2
        9"; FPKM "0.0000000000"; frac "0.000000"; conf_lo "0.000000"; conf_hi "0.000000"; cov "0.000000";
3>    2 chrI    Cufflinks   exon    1738651 1738674 1   +   .   gene_id "Y71G12B.29"; transcript_id "Y71G12B.29"; 
        exon_number "1"; FPKM "0.0000000000"; frac "0.000000"; conf_lo "0.000000"; conf_hi "0.000000"; cov "0.0000
        00";  
      3 chrI    Cufflinks   transcript  111292  111425  1   +   .   gene_id "F53G12.12"; transcript_id "F53G12.12"
        ; FPKM "0.0000000000"; frac "0.000000"; conf_lo "0.000000"; conf_hi "0.000000"; cov "0.000000";

FPKM is 0.

why ?

[blanco]

It is not unusual (I think) that many transcripts have an FPKM of value 0 - just means that that transcript is not expressed.

However if all transcripts have an FPKM value of 0 then something is wrong. My first guess would be that the chromosome names in the reference does not match the chromosome names in the annotation.