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From Rna-Seq Reads/Alignments Data To Gff Files

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,

rna-seq gff
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updated by Biostar Biostar • written by Bioinfguy • Bioinfguy

2 answers

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.

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written by JC JC

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,

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written by Bioinfguy • Bioinfguy

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

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written by Mikael Huss Mikael Huss

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