Hi Everyone, I'm new to RNAseq and I'm trying to run cuffmerge but I'm encountering the following error message:

[Mon Aug 29 12:09:13 2016] Beginning transcriptome assembly merge

[Mon Aug 29 12:09:13 2016] Preparing output location ./merged_asm/

Traceback (most recent call last):

File "/software/cufflinks/2.2.1/bin/cuffmerge", line 580, in <module>

  sys.exit(main())

File "/software/cufflinks/2.2.1/bin/cuffmerge", line 538, in main

  gtf_input_files = test_input_files(transfrag_list_file)

File "/software/cufflinks/2.2.1/bin/cuffmerge", line 268, in test_input_files

  g = open(line,"r")

IOError: [Errno 2] No such file or directory: './path/to/1_clout/transcripts.gtf'

My cuffmerge command is:

cuffmerge -p 8 -g /path/to/gff-file.gff -s /path/to/genome.fa assemblies.txt

and assemblies.txt is a text file that looks like:

./path/to/1_clout/transcripts.gtf

./path/to/2_clout/transcripts.gtf

./path/to/3_clout/transcripts.gtf

./path/to/4_clout/transcripts.gtf

./path/to/5_clout/transcripts.gtf

./path/to/6_clout/transcripts.gtf

It seems to me that cuffmerge can't find the .gtf files made by cufflinks. Is my syntax wrong? I used a reference gff file when running tophat and cufflinks and I'm wondering if my transcripts.gtf files are now wrong?

Thanks for your help!