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script to write the path of all the output files of Cufflinks in a text file for Cuffmerge?

Hello,

With cufflinks command I have many gtf files as outputs. For Cuffmerge I created a text file in which I gave the path to all text files.

/A/A_GRCh37.gtf
/B/B_GRCh37.gtf
/C/C_GRCh37.gtf
/D/D_GRCh37.gtf
/E/E_GRCh37.gtf
/F/F_GRCh37.gtf

I have more than 100 gtf files. How can I write the path of all gtf files in a text file for Cuffmerge?

A small code is needed for creating text file and writing the paths of all the gtf files

rna-seq cuffmerge cufflinks
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updated by Arup Ghosh Arup Ghosh • written by Biologist Biologist

1 answer

If your gtf files are in the same directory structure as you mentioned you can use the following command to get a text file with all the assembly file locations.

ls */*_GRCh37.gtf > assembly.txt
• 0 views • link
written by Arup Ghosh Arup Ghosh

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