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Old 03-18-2013, 02:00 AM   #1
Location: Nanjing, China

Join Date: Mar 2013
Posts: 10
Default Problem about splicing.diff from cuffdiff

This problem has puzzled me one week long!
I followed the workflow:Tophat - Cufflinks - Cuffmerge - Cuffdiff,and everything is OK except the splicing.diff file generated by cuffdiff. After running Cuffdiff, it print "Performed 0 splicing tests", and splicing.diff file is filled up with LOWDATA and NOTEST without even one OK. I used merged.gtf as input, which has tss_id and p_id. And I also tried to use combined.gtf from Cuffcompare as input, but the result was the same. Can anyone help me?

Here is my command:
1).cuffmerge -o ./merged_asm/ -g genes.gtf -s genome.fa -p 8 assemblies.txt
2).cuffdiff -o ./diff_asm/ -b ./genome.fa -p 8 -L L1,L2,L3 -u ./merged_asm/merged.gtf ./Sample_out/accepted_hits.bam ./4h_out/accepted_hits.bam ./S48h12_out/accepted_hits.bam

Then is some lines of my merged.gtf
PHYCAscaffold_1	Cufflinks	exon	41144	42265	.	+	.	gene_id "XLOC_000001"; transcript_id "TCONS_00000001"; exon_number "1"; oId "transcriptId502542"; nearest_ref "proteinId502542"; class_code "o"; tss_id "TSS1";
PHYCAscaffold_1	Cufflinks	exon	41195	41689	.	+	.	gene_id "XLOC_000001"; transcript_id "TCONS_00000002"; exon_number "1"; oId "proteinId502542"; contained_in "TCONS_00000001"; nearest_ref "proteinId502542"; class_code "="; tss_id "TSS1"; p_id "P1";
PHYCAscaffold_1	Cufflinks	exon	42789	45015	.	+	.	gene_id "XLOC_000002"; transcript_id "TCONS_00000003"; exon_number "1"; oId "transcriptId502544"; nearest_ref "proteinId502544"; class_code "="; tss_id "TSS2"; p_id "P2";
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