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Thread Tools |
09-21-2011, 07:40 AM
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#1 |
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Member
Location: Beijing, China Join Date: Oct 2010
Posts: 30
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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 ? |
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09-19-2012, 03:43 AM
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#2 |
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Member
Location: Iceland Join Date: Apr 2012
Posts: 28
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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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