How do I merge .gtf files

[Milestailsprowe]

Hello. I'm trying to merge transcript.gtf I got from using cufflinks. Can someone explain how to make the assemblies.txt file

[GenoMax]

You can make the assemblies.txt file using an editor such that it contains paths (relative or full) to the transcripts.gtf files generated by cufflinks runs.

If you followed the same logic as described in the "Nature protocols" paper these would be in the "sample_ID_clout" folder.

$ more assemblies.txt

/path_to/sample1_clout/transcripts.gtf
/path_to/sample2_clout/transcripts.gtf
/path_to/sample3_clout/transcripts.gtf
/path_to/sample4_clout/transcripts.gtf
/path_to/sample5_clout/transcripts.gtf

You get the idea.

[Milestailsprowe]

So... If I have two transcript.gtf files I use what command? Just more assemblies.txt?

[GenoMax]

You put the locations (file paths) of those two transcript.gtf files inside a single file and call that file "assemblies.txt".

Assemblies.txt file should contain file locations of all transcripts.gtf files you are trying to merge.