i have some problem related to cuffidiff output, i used this command for replicates:
cuffdiff -o diff_out -b genome/genome.fa -p 10 -L CT,SS --total-hits-norm -u cuffmerge_experiment/merged.gtf tophat_exp/tophat_exp1/accepted_hits.bam,tophat_exp/tophat_exp2/accepted_hits.bam tophat_exp/tophat_exp3/accepted_hits.bam,tophat_exp/tophat_exp4/accepted_hits.bam
in my output file i found gene column is empty:
TCONS_00000001 XLOC_000001 - C11044824:403-1007 CT SS OK 4.25634 4.05292 -0.0706522 0.148488 0.881958 0.999985 no
TCONS_00000002 XLOC_000002 - C11047824:1-1042 CT SS OK 4.96333 5.54938 0.161018 -0.40853 0.682884 0.999985 no
TCONS_00000003 XLOC_000003 - C11048020:0-588 CT SS OK 3.66925 4.25115 0.212368 -0.422853 0.672403 0.999985 no
TCONS_00000004 XLOC_000004 - C11048338:216-588 CT SS OK 0.795992 0.604691 -0.396557 0.258201 0.796252 0.999985 no
TCONS_00000005 XLOC_000005 - C11049822:426-1035 CT SS OK 0.359691 0.790309 1.13566 -0.675737 0.499208 0.999985 no
i cant understand how can be its possible, if any one have suggestion please guide me.
upto cuffmerge i found gene in my file like this:
C11111420 Cufflinks exon 726 1304 . - . gene_id "XLOC_000033"; transcript_id "TCONS_00000034"; exon_number "1"; oId "Ca_28192"; nearest_ref "Ca_28192"; class_code "="; tss_id "TSS33"; p_id "P11";
C11112120 Cufflinks exon 391 1218 . + . gene_id "XLOC_000034"; transcript_id "TCONS_00000035"; exon_number "1"; oId "Ca_27742"; nearest_ref "Ca_27742"; class_code "="; tss_id "TSS34"; p_id "P12";
C11112120 Cufflinks exon 1577 1657 . + . gene_id "XLOC_000034"; transcript_id "TCONS_00000035"; exon_number "2"; oId "Ca_27742"; nearest_ref "Ca_27742"; class_code "="; tss_id "TSS34"; p_id "P12";
C11112120 Cufflinks exon 1929 2126 . - . gene_id "XLOC_000035"; transcript_id "TCONS_00000036"; exon_number "1"; oId "Ca_27743"; nearest_ref "Ca_27743"; class_code "="; tss_id "TSS35"; p_id "P13";
C11115550 Cufflinks exon 6 533 . + . gene_id "XLOC_000036"; transcript_id "TCONS_00000037"; exon_number "1"; oId "Ca_27676"; nearest_ref "Ca_27676"; class_code "="; tss_id "TSS36"; p_id "P14";
C11115550 Cufflinks exon 2561 2800 . - . gene_id "XLOC_000037"; transcript_id "TCONS_00000038"; exon_number "1"; oId "Ca_27677"; nearest_ref "Ca_2767
so how can be its possible that i didn't find in cuffdiff output. please contact on my email address thakkar.bjl@gmail.com
It seems that you don't use a reference GFF/GTF file containing known transcripts and gene names.
You should use a gff/gtf file ( for example the genes.gtf file in one of the archives here http://tophat.cbcb.umd.edu/igenomes.shtml ) in the cuffcompare step:
cuffcompare -r genes.gtf <input1.gtf> [<input2.gtf> .. <inputN.gtf>]}
It produces a cuffcmp.combined.gtf file that you can use in the cuffdiff step.
i also used cuffcmp.combined.gtf file in that, i used .gff file then reference fasta file and my cufflink output transcripts.gtf file but it also give same result, in gene column it is like "-" .i tried a lot. thanks for your reply.
my gff file look like this.
Ca8 GLEAN mRNA 37786 42033 0.760266 - . ID=Ca_11937;evid_id=GAR_10012294;
Ca8 GLEAN CDS 41914 42033 . - 0 Parent=Ca_11937;
Ca8 GLEAN CDS 41781 41843 . - 0 Parent=Ca_11937;
Ca8 GLEAN CDS 41556 41690 . - 0 Parent=Ca_11937;
Ca8 GLEAN CDS 41300 41473 . - 0 Parent=Ca_11937;
Ca8 GLEAN CDS 41118 41222 . - 0 Parent=Ca_11937;
Ca8 GLEAN CDS 40879 40912 . - 0 Parent=Ca_11937;
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cross posted on http://seqanswers.com/forums/showthread.php?t=36211