Question: isoforms with cufflinks
0
gravatar for lubaa88
4.0 years ago by
lubaa880
lubaa880 wrote:

i used the cufflinks tool to create the isoforms. how can i know how many isoforms were created?

 

thank you

rna-seq cufflinks gff galaxy • 1.1k views
ADD COMMENTlink modified 4.0 years ago • written 4.0 years ago by lubaa880
0
gravatar for Jennifer Hillman Jackson
4.0 years ago by
United States
Jennifer Hillman Jackson25k wrote:

Hello,

GTF datasets are a type of tabular data. You should be able to use the tools that count up rows in a tabular/text file, or summarize by columns, without an issue. See the tool groups: Text Manipulation, Filter and Sort, and Join, Subtract and Group to start with.

If the dataset is not recognized by a tool for some reason (it only accepts 'tabular' datasets), make a copy of the dataset and change the datatype to "tabular" to work with it. The copy data function is in the History menu. To reassign datatype, click on the pencil icon for a dataset and make changes in the form that appears in the center panel.

Thanks, Jen, Galaxy team

ADD COMMENTlink written 4.0 years ago by Jennifer Hillman Jackson25k
0
gravatar for lubaa88
4.0 years ago by
lubaa880
lubaa880 wrote:

sorry but i still dont know how to do this.

i have 5 samples and i need to know how much isoforms assembled to each gene and how much genes were assembled.

i am looking at this database: cuffdiff:isoforms read group tracking

maybe this is wrong file and i need to look at another file?

i really need your help.. this is the last level in my project.. 

thank you very much

ADD COMMENTlink written 4.0 years ago by lubaa880

HOW DO i GET THE GTF DATSET FOR CDC20. I AM KIND OF LOST, AS I AM FIRST TIME USER.

ADD REPLYlink written 3.7 years ago by smn536010
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