Question: blank values for some rows in gene column in cuffdiff output
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4.6 years ago by
EpiExplorer90
New Zealand
EpiExplorer90 wrote:

Hi, I find some blank values in some rows for gene column in gene_exp.diff file and those genes are in the list of significantly expressed genes. Why does cuffdiff give blank values? And how can I get a gene name for those rows?

I am pasting few rows here to give an idea how the output looks like: test_id gene_id gene locus sample_1 sample_2 status value_1 value_2 log2(fold_change) test_stat p_value q_value significant

XLOC_005222 XLOC_005222 - 1:189333379-189333794 C1 C2 OK 0 0.536239 inf #NAME? 0.0005 0.0444788 yes

Here the gene column has no name but just "-". I tried to look for this record in the merged transcript assembly file(generated after cufflinks and cuffmerge) and found the record below: 1 Cufflinks exon 189333380 189333794 . - . gene_id "XLOC_005222" transcript_id "TCONS_00023282" exon_number "1" oId "CUFF.2661.1" class_code "u" tss_id "TSS12233"

In this record the gene name column shows- oId "CUFF.2661.1. Does this mean this gene is novel according to cufflinks assembly prediction?( For the records from known genes, gene name column has gene symbols in place of the cufflink ids as shown above.)

Can anyone help with this please?

Thanks.

rna-seq • 1.1k views
ADD COMMENTlink modified 4.6 years ago • written 4.6 years ago by EpiExplorer90

I am pasting few rows here to give an idea how the output looks like: test_id gene_id gene locus sample_1 sample_2 status value_1 value_2 log2(fold_change) test_stat p_value q_value significant

XLOC_005222 XLOC_005222 - 1:189333379-189333794 C1 C2 OK 0 0.536239 inf #NAME? 0.0005 0.0444788 yes

Here the gene column has no name but just "-". I tried to look for this record in the merged transcript assembly file(generated after cufflinks and cuffmerge) and found the record below: 1 Cufflinks exon 189333380 189333794 . - . gene_id "XLOC_005222" transcript_id "TCONS_00023282" exon_number "1" oId "CUFF.2661.1" class_code "u" tss_id "TSS12233"

In this record the gene name column shows- oId "CUFF.2661.1. Does this mean this gene is novel according to cufflinks assembly prediction?( For the records from known genes, gene name column has gene symbols in place of the cufflink ids as shown above.)

Can anyone help with this please?

ADD REPLYlink modified 4.6 years ago • written 4.6 years ago by EpiExplorer90
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Please edit your question and add this information. The instructions to do this are here: C: How do I ask a question on Biostars?

ADD REPLYlink written 4.6 years ago by _r_am32k
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