Question: From Rna-Seq Reads/Alignments Data To Gff Files
0
gravatar for Bioinfguy
7.0 years ago by
Bioinfguy30
Germany
Bioinfguy30 wrote:

Hello,

Does any one know how can I create gene models (GFF files) from RNA-seq reads or alignments ?

Inputs: RNA-seq reads and reference genome, I also have the bam mapping file produced from Tophat. I used cufflinks, but I need another tool to compare between them.

Thank you in advance.

Best,

gff rna-seq • 2.5k views
ADD COMMENTlink modified 2.8 years ago by Biostar ♦♦ 20 • written 7.0 years ago by Bioinfguy30
1
gravatar for JC
7.0 years ago by
JC7.8k
Mexico
JC7.8k wrote:

Dear Bioinfguy, cufflinks creates the gene models in GFF format (transcripts.gtf), if you want to compare different data sets, use cuffdiff. Maybe you can explain a little more what do you really want to do.

ADD COMMENTlink written 7.0 years ago by JC7.8k

Thank you for the answer I would like to compare different programs whose input is RNA-seq reads or alignments and its output id GFF fils so I can compare them with cuffcompare. I need to decide which program is the best to use in my pipeline. I used cufflinks, and I need more programs whose output i comparable with cufflinks's output.

Thanks,

ADD REPLYlink written 7.0 years ago by Bioinfguy30
1
gravatar for Mikael Huss
7.0 years ago by
Mikael Huss4.6k
Stockholm
Mikael Huss4.6k wrote:

You can try Scripture from Broad Institute. It lists GFF as one of its output formats.

ADD COMMENTlink written 7.0 years ago by Mikael Huss4.6k
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