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Forum: RNA Sequencing 05-23-2014, 12:54 PM
Replies: 0
Views: 1,056
Posted By vramnarine
Cuffcompare : Reference or Merged transcriptome

Hi All ,

I would like to run cuffcompare but confused about what reference to supply it?

With my workflow I run cuffmerge (after cufflinks) WITH an annotated reference supplied, so when I run...
Forum: Bioinformatics 05-22-2014, 07:20 PM
Replies: 2
Views: 3,510
Posted By vramnarine
Have either of you found an answer to this...

Have either of you found an answer to this question?

Ive posted a similar thread here:
http://seqanswers.com/forums/showthread.php?t=43523

No response yet.

The parameters seem redundant and...
Forum: RNA Sequencing 05-22-2014, 11:41 AM
Replies: 0
Views: 2,000
Posted By vramnarine
Cuffnorm Normalization: Per condition or across all samples ?

Hi All

I am using the new workflow of:

Cufflinks -> Cuffmerge -> Cuffquant -> Cuffnorm

When supplying a sample sheet (using parameter: --use-sample-sheet) , I must designate conditions per...
Forum: RNA Sequencing 05-22-2014, 11:39 AM
Replies: 0
Views: 1,562
Posted By vramnarine
Cuffnorm Parameters : total hits vs. compatible hits

Hi All

I am using the new workflow of:

Cufflinks -> Cuffmerge -> Cuffquant -> Cuffnorm

I am confused with the 'hits' parameters within cuffnorm:
CHOICE 1 --compatible-hits-norm: count hits...
Forum: RNA Sequencing 05-22-2014, 11:37 AM
Replies: 2
Views: 3,616
Posted By vramnarine
Cufflinks, Cuffquant and Cuffdiff Parameters : multi-read and frag-bias correction

Hi All,

I am using the new Cufflinks workflow of:

Cufflinks -> Cuffmerge -> Cuffquant -> Cuffdiff

Within cufflinks I use the following parameters:
--frag-bias-correct
--multi-read-correct
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