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how can I output the merged.gtf of cuffmerge in another folder ?

Dear all,

I am running the following command to merge all the GTFs from different samples into a merged GTF:

cuffmerge --ref-gtf celegans.gtf --ref-sequence celegans.fa assemblies.txt -o pooled/

It outputs the merged.gtf file in merged_asm/ folder. Does anybody know how I can change the folder in which the file is written?

Thanks.

Best,

Cristian.

cuffmerge cufflinks gtf alignment assembly
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written by biomagician biomagician

That is a design choice on part of the developers.

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written by GenoMax GenoMax

So, it's not possible to change the folder? :=(

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written by biomagician biomagician

so I am just moving the folder with Unix command 'mv'.

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written by biomagician biomagician

Do it once the run completes.

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written by GenoMax GenoMax

What do you mean by run? The cuffmerge command or after the cuffdiff?

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written by biomagician biomagician

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