Cuffmerge error(?) for RNA-seq

Question

[bioinfo]

Hi, I'm currently doing cuffmerge to merge all transcripts.gtf files. After saving all path of transcripts.gtf at nano text editor, my command line was:

./cuffmerge -o merged_gtf -g reference.gtf -s reference.fsa -p 2 assembled.txt

and result command line was:

[Fri Jan 19 17:48:19 2018] Beginning transcriptome assembly merge
----------------------------------------------
[Fri Jan 19 17:48:19 2018] Preparing output location merged_gtf/
[Fri Jan 19 17:48:19 2018] Converting GTF files to SAM

That's all, and I couldn't find the merged.gtf file even merged_gtf folder was generated containing logs, tmp sub-folders. And logs folder contains just 'logs' file and tmp folder has nothing. I don't know about problem.

[natallah]

What does your assembled.txt look like? Is each path to the gtf files on a different line?

[Ram]

This is a follow up question, not an answer. It belongs as a comment on OP's question. I've moved it there for now, but please be more careful in the future.

Read the posts under https://www.biostars.org/t/how-to/ to get more information on how to use the forum better.

[bioinfo]

Thank you for replying me. Yes, I designated all gtf files in separate.

[bioinfo]

And an error I got was "gtf_to_sam can not found on this system. Did you include your PATH?" like this.

[Kevin Blighe]

Yes, you have to add it to the PATH variable. I have this written in my most recent experiment's notes where I was using Cufflinks:

#Add cufflinks to PATH, as cuffmerge looks for gtf_to_sam
PATH=/Programs/cufflinks-2.2.1.Linux_x86_64/:$PATH

[bioinfo]

Ohhh.. I'm getting data using cuffmerge!!!!!!! Thank you so much! I had wasted time solving this... Now I solved!! Thank you!

[Kevin Blighe]

Great - glad to have helped

[bioinfo]

Thank you very much! But I'm a quite novice in this field.. Could you tell me more specifically? Do I just type that text you wrote in a terminal? Or should I need to write after orange"$PATH" you wrote?

[Kevin Blighe]

Yes, you have to type that each time that you want to run Cufflinks (you can just include it as part of your code) - it is good practice to keep a separate script text file for each project on which you're working. Helps to be organised.

More specifically, you should locate the directory in which the gtf_to_sam executable is stored, and then use that directory location in the PATH command.

For example, if (on your hard-disk), gtf_to_sam is located in /home/bioinfo/cufflinks/, then your command should be:

PATH=/home/bioinfo/cufflinks/:$PATH

[bioinfo]

Thank you! I can much more understanding thanks to you. So, now, my cufflinks-2.2.1.Linux_x86_64 folder is in

/home/bioinfo/Downloads/cufflinks-2.2.1.Linux_x86_64

So, I should type

cd /home/bioinfo/Downloads/cufflinks-2.2.1.Linux_x86_64

and just type the command that you mentioned at directory

/home/bioinfo/Downloads/cufflinks-2.2.1.Linux_x86_64$ PATH=/home/bioinfo/Downloads/cufflinks-2.2.1.Linux_x86_64:$PATH

Am I right..?

[Kevin Blighe]

Yep, well, you just need:

PATH=/home/bioinfo/Downloads/cufflinks-2.2.1.Linux_x86_64:$PATH

[Ram]

Please use the formatting bar (especially the code option) to present your post better. I've done it for you this time.

[bioinfonewbie]

hi i have same problem. this is my code

usr/local/sw/cufflinks-2.2.1.Linux_x86_64/cuffmerge -g transcripts.gtf -s chr22.fa -p 8 assemlies.txt

and give me this error

Converting GTF files to SAM
        [FAILED]
Error: gtf_to_sam not found on this system.  Did you forget to include it in your PATH?

i cant understand your solutions and create a sh file like this

#!/bin/bash
PATH=$PATH:/usr/local/sw/cufflinks-2.2.1.Linux_x86_64/gtf_to_sam
/usr/local/sw/cufflinks-2.2.1.Linux_x86_64/cuffmerge -g transcripts.gtf -s chr22.fa -p 8 assemlies.txt

but it give same error

[Kevin Blighe]

Hi, you may want to try this:

export PATH="/usr/local/sw/cufflinks-2.2.1.Linux_x86_64/:$PATH"