sampleName_count column in Cuffdiff output file

I ran Cuffdiff on GenePattern. What does the sampleName_count column in the genes.count_tracking output file represent?

rna-seq

• 1,582 views • link

updated 4.1 years ago by Ram

• written 11.3 years ago by devorah.fialkoff •

0 answers

No answers yet.

More posts like this

Cuffdiff Output file question
written 3.0 years ago by sumitra.20 •

Hi, I followed through the tophat-cufflink pipeline for my test data (3 samples). I merged all my samples with cuffmerge and ran cuffdiff as below: …
ssGSEA for beginners
written 5.7 years ago by mk.gill •

Dear ssGSEA users, I am a biologist trying to do RNA-seq analysis for breast cancer PanCancer Atlas dataset obtained from cbioportal. I have generated gene …
Question: Cuffdiff output file gene_exp.diff has only one gene but isoforms_exp.diff has thousands …
written 6.3 years ago by SamuelWarner •

Hi - hope everyone is holding up in these days! I am doing RNA-seq analysis on some plant data (over different time points) and ran …
about cuffdiff input and parameters
written 7.8 years ago by yaminivadapally •

i have 120 sample in which 60 are controls and 60 are diseased, i ran tophat, cufflinks and cuffmerge i have merged_asm.gtf file which is …
CUFFDIFF giving empty CDS.DIFF files
written 8.5 years ago by Rose •

Hi, I ran cuffdiff using c.elegans( WBcel235) gtf file on two groups of bam, ech having three replicates. The output produced by cuffdiff had empty …
Cuffnorm: which output file should I use
written 9.0 years ago by ha.hassanzadeh •

Hello Biostars, I'm trying to use `cuffnorm` to normalize the `cuffquant` results. I'm getting these output files: - cds.count_tracking - cds.read_group_tracking - genes.fpkm_tracking - isoforms.count_tracking …
input of cummerbund
written 9.1 years ago by dimitrischat

Hello all. I finally ran cuffdiff successfully, but now i wanna run cummeRbund on galaxy. i have no idea which of the outputs i must …
Empty Cuffdiif Output except Gene Differential expression testing
written 9.3 years ago by benjyrolls

Hello I am running a Cuffdiff on two separate conditions of a file. all outputs seem to be empty except the gene differential expression output …
Cuffdiff secondary alignments (lower counts?)
written 11.3 years ago by jomaco

Hi, When I use the option --report-secondary-alignments in TopHat, cuffdiff reports that there are fewer fragments mapping to some genes in the genes.count_tracking file. Without …
Raw read count on Cuffdiff
written 11.4 years ago by 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 …