In addition, you might want to explain why you need that gtf file. I think most commonly you will download a gtf file, for example from Ensembl, which you will use to annotate and quantify your RNA-seq data.
In spite of the lack of information in your question, I assume that you want to perform a transcriptome annotation using RNA-Seq data. As you have mentioned, Cufflinks can do the job, but there are also another tools for doing it. I'd recommend you to read a little bit the literature, get familiar with the different methods and tools, find any paper with comparisons of the different computational methods... etc. For sure you'll find also great tutorials explaining how to perform a transcriptome annotation.
Here is a nice piper describing transcriptome annotation using RNA-Seq data and some different strategies to address the question.
Hi Everyone, I am working in RNA-seq data analysis, I tried Cufflinks for Transcript Quantification from STAR mapped BAM file, but its not showing any …
Aslam o Alikum I have Bam files of non human genome. Now I want to generate annotation files(mappbility&gcWinds) for readDepth Tool to detect cnvs, Please …
I used tophat-cufflinks pipeline for RNA-seq analysis. In the output file, there is only temporarily test ids such as XLOC_000001. Since I use GRCh38 annotation …
<p>Hi Guys</p> <p>Keeping it short I want to know which is a better approach for building transcripts models using cufflinks.</p> <p>If I have an older …
<p>I have a question about using cufflinks for transcriptome assembly. Once we generate a new gene model/transcriptome for a specie what are the various ways …
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In addition, you might want to explain why you need that gtf file. I think most commonly you will download a gtf file, for example from Ensembl, which you will use to annotate and quantify your RNA-seq data.
In spite of the lack of information in your question, I assume that you want to perform a transcriptome annotation using RNA-Seq data. As you have mentioned,
Cufflinkscan do the job, but there are also another tools for doing it. I'd recommend you to read a little bit the literature, get familiar with the different methods and tools, find any paper with comparisons of the different computational methods... etc. For sure you'll find also great tutorials explaining how to perform a transcriptome annotation.Here is a nice piper describing transcriptome annotation using RNA-Seq data and some different strategies to address the question.