Raw read count on Cuffdiff

Question

[devorah.fialkoff]

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

[karl.stamm]

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.

[devorah.fialkoff]

Thank you all for your help.

What does the sampleName_count column in the genes.count_tracking output file represent?

Answer 1

[kangyueapril]

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 information 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.

[karl.stamm]

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

[kangyueapril]

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.

[scchess]

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