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Hi,
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
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
Code:
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";