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.
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cufflinks output against annotation file
hello, everyone,
i run the cufflinks to calculate the RPKM(or FPKM) for annotated genes for C.elegans.
i type in the command.
Code:cufflinks -p 8 -G WormBase190/ce6_sangerRNA.gtf N2.sort.bam
however, the output is like this.
Code: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";
why ?Tags: None
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