From Rna-Seq Reads/Alignments Data To Gff Files

Question

[Bioinfguy]

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,

Answer 1

[JC]

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.

[Bioinfguy]

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,

Answer 2

[Mikael Huss]

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