cuffmerge - from wrong not indexed files?

[Marys]

hi Everyone,
I am new in RNAseq analysis. I have run tophat then cufflinks, and now I wnat to run cuffmerge, but I have found this problem:

# cuffmerge -p 4 -g /path/to/genes.gtf -s /path/to/genome.fa /path/to/assemblies.txt

[Thu Oct 23 13:18:51 2014] Beginning transcriptome assembly merge
-------------------------------------------

[Thu Oct 23 13:18:51 2014] Preparing output location ./merged_asm/
Traceback (most recent call last):
File "/usr/bin/cuffmerge", line 580, in <module>
sys.exit(main())
File "/usr/bin/cuffmerge", line 530, in main
transfrag_list_file = open(args[0], "r")
IOError: [Errno 2] No such file or directory: '/home/michalina/BAM_SAM_tophat_samtools/TS2/assemblies.txt


I have no idea what is going wrong. My cufflinks were wrong? gtf or fa references file are not appropriate? hese are the same reference files that I use for previous analysis (tophat, cufflinks).

many thanks for any commnet or advise
M.

[GenoMax]

Have you made a list of the GTF files from your cufflinks assemblies and then put the names in the "assemblies.txt" file? Your error is about this file not being present.

From Cuffmerge help:

<assembly_list.txt> Text file "manifest" with a list (one per line) of GTF files that you'd like to merge together into a single GTF file.

[Marys]

Hi Genomax,

no I haven't, how can I do this? could you tell me?

I did something like this:
cat /home/michalina/BAM_SAM_tophat_samtools/TS/transcripts.gtf /home/michalina/BAM_SAM_tophat_samtools/TS2/transcripts.gtf > asseblies.txt

but I was afraid it was wrong.

Honestly, I am new one in all these things...

[GenoMax]

Make a file called "assemblies.txt" and put these two lines in it (use a text editor):

/home/michalina/BAM_SAM_tophat_samtools/TS/transcripts.gtf
/home/michalina/BAM_SAM_tophat_samtools/TS2/transcripts.gtf

[Marys]

wow! many thanks!!! that was that much simple