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

Question

[Biologist]

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

Answer 1

[Arup Ghosh]

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