Question: Error using stringtie merge
0
gravatar for cwj6
2.0 years ago by
cwj60
cwj60 wrote:

I'm trying to merge 6 gtf files I made with stringtie. I've written their file names in a .txt file in the proper format and named it mergelist.txt. The files I want to merge are in the directory I'm currently using. When I try to run:

stringtie --merge -p 4 -G /home/chris/Desktop/Mus_musculus_UCSC_mm10/Mus_musculus/UCSC/mm10/Annotation/Genes/genes.gtf -o stringtie_merged.gtf mergelist.txt

I get the error:

Error: cannot find file 'IP1t_stringtie.gtf' and mergelist.txt does not look like GFF!

The IP1t gtf is the first file in the list of 6 gtfs. All appear to be formatted validly if I inspect them, and they're straight out of stringtie itself. I'm sure I'm making a simple mistake, but I can't figure out what it is and googling these errors hasn't turned up anything. Thanks in advance for any help.

rna-seq • 1.6k views
ADD COMMENTlink modified 23 months ago by megan.chan0 • written 2.0 years ago by cwj60

Can you try the following? Some programs are sensitive to the order of options given.

stringtie --merge -p 4 -o stringtie_merged.gtf -G /home/chris/Desktop/Mus_musculus_UCSC_mm10/Mus_musculus/UCSC/mm10/Annotation/Genes/genes.gtf  mergelist.txt

GTF files listed one per line in mergelist.txt, correct?

ADD REPLYlink written 2.0 years ago by genomax78k

Thanks for the reply. I got the same error after flipping around the -g and -o commands, unfortunately. And yeah, the gtf files are all on separate lines with no other formatting.

ADD REPLYlink written 2.0 years ago by cwj60

Can you try adding full path to the GTF file names in your mergelist.txt?

ADD REPLYlink written 2.0 years ago by genomax78k

Yup, I get the same error but with the full path instead of just the file name. Maybe I'll just start from the beginning and make all new gtf files.

ADD REPLYlink written 2.0 years ago by cwj60
1
gravatar for anngrenda
23 months ago by
anngrenda10
anngrenda10 wrote:

Hello.

I am currently facing the exact same error. Any luck with your mergelist.txt yet? What was the problem after all?

ADD COMMENTlink written 23 months ago by anngrenda10

I never actually found a solution to this (or related) problems even after re-doing the analysis from the beginning. What I ended up doing was just bypassing the merge step and going straight to stringtie -eB just using the basic gene.gtf as the -G input, not a merged .gtf file. So for example:

stringtie -e -B -p 4 -G /home/chris/Desktop/tacr3_rnaseq/Genes/genes.gtf -o ballgown/i1/i1_stringtieout.gtf i1samout.bam

After analyzing with ballgown I got roughly similar outputs as I did with tophat/bowtie/cuffdiff, so I'm assuming that'll work OK.

ADD REPLYlink modified 23 months ago • written 23 months ago by cwj60
0
gravatar for megan.chan
23 months ago by
megan.chan0
megan.chan0 wrote:

Also having the same issue, I was able to merge successfully earlier this week with a different set of GTF files, but they were generated in the exact same way. This leads me to believe the problem is actually in the GTF files rather than mergelist.txt. Did you figure out why?

ADD COMMENTlink written 23 months ago by megan.chan0

Solved my issue. I was using the wrong version of the reference file (-G).

ADD REPLYlink written 23 months ago by megan.chan0
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