Question: Raw read count on Cuffdiff
0
gravatar for devorah.fialkoff
5.7 years ago by
European Union
devorah.fialkoff0 wrote:

Hi,

I'm very new to RNA-seq analysis.
I ran Cuffdiff on GenePattern, and I wanted to know how I can get the raw read count for each gene. Can I get this information from any of the output files of Cuffdiff?

Thanks,
Debbie

rna-seq • 3.1k views
ADD COMMENTlink modified 5.7 years ago • written 5.7 years ago by devorah.fialkoff0

The Bowtie-Tophat-Cufflinks suite does not report raw counts. It estimates RPKM per isoform, which is not a raw count. You can get gene expression data from cufflinks, but it wont be count data.

ADD REPLYlink written 5.7 years ago by karl.stamm3.9k
0
gravatar for kangyueapril
5.7 years ago by
kangyueapril80
United States
kangyueapril80 wrote:

Before you run cuffdiff, you must have assembled the transcripts and calculated the abundances for every gene and transcript using cufflinks. So you can find the expression informatiom in cufflinks output files. But be careful, you may get FPKM or RPKM instead of  raw count from cufflinks. If you want get raw count information you can try HTSeq or RSEM.

ADD COMMENTlink written 5.7 years ago by kangyueapril80

RSEM does not generate count information, it takes counts as input.  HTSeq will count reads.

ADD REPLYlink written 5.7 years ago by karl.stamm3.9k

RSEM  not just can be use to find  DEGs, but also can assemble transcripts like cufflinks or HTSeq. In the output file after assemble transcripts using RSEM, it give expression value in counts, FPKM and TPM. Then it will use counts as input when you do DEGs found. 

ADD REPLYlink written 5.7 years ago by kangyueapril80

We're asking for the count table, not the RSEM stuffs.

ADD REPLYlink written 4.9 years ago by SmallChess540
0
gravatar for devorah.fialkoff
5.7 years ago by
European Union
devorah.fialkoff0 wrote:

Thank you all for your help.
What does the sampleName_count column, in the genes.count_tracking output file represent?

ADD COMMENTlink written 5.7 years ago by devorah.fialkoff0
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