Problems With Cuffmerge

Hi everyone,

I'm trying to use cuffmerge but I get the following error message:

[Thu Oct 27 13:47:16 2011] Converting GTF files to SAM [FAILED] Error: gtftosam not found on this system. Did you forget to include it in your PATH?

My command line is:

/storage/app/cufflinks-1.0.3/cufflinks-1.0.3.Linuxx8664/cuffmerge -g /storage/data/natasha/gtf/miRNArelatedtracksknownmiRNAshg18.gtf -s /storage/data/natasha/chrsfa/hg18norandomnohap.fa assembles_cancer.txt

I've tested the gtftosam program and it worked fine.

Do I have do put something else in my command line? I've read the manual, but I couldn't find anything...

thanks in advance!

cufflinks cuffmerge error

• 4,832 views • link

updated 14.8 years ago by Sukhi Singh

• written 14.8 years ago by Natasha •

1 answer

Problem with the PATH variable, specifying gtftosam should solve it. Taking an excerpt from your own reply as a reference from this seqanswers post,

thanks for the replys! I've already fixed it. It was a problem with my bash file, nothing to do with cufflinks... sorry!

• 2 views • link

written 14.0 years ago by Sukhi Singh

More posts like this

Cuffmerge and cuffdiff error
written 7.8 years ago by carrilloarzola3 •

I am trying to use cuffmerge in order to merge 4 transcript assemblies that I have obtained through cufflinks. The data has worked through tophat, …
cuffmerge output question
written 9.2 years ago by Biologist

Hello, I used cuffmerge to merge all assemblies to create a single merged transcriptome annotation. cufflinks version 2.2.1 cuffmerge -g Homo_sapiens.GRCh37.82.chr_patch_hapl_scaff.gtf -s human_g1k_v37_decoy_bowtie2 -p 8 …
Error: duplicate GFF ID 'ENSMUST00000105372' encountered! [FAILED] Error: could not execute cuffco…
written 9.8 years ago by jolin0701-dy

I just got an error from cuffmerge $ ~/programs/cufflinks-2.1.1.OSX_x86_64/cuffmerge -g ~/GRCm38_86/mouse.gtf -s ~/GRCm38_86/mouse.fa assemblies.txt [Mon Oct 10 19:28:48 2016] Beginning transcriptome assembly merge ------------------------------------------- [Mon …
Cuffmerge cannot find transcripts.gtf files
written 9.9 years ago by calubr •

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 …
Cuffmerge BAM error
written 10.3 years ago by jenkelly •

Dear forum I have run cuffmerge on multiple gtf files generated by cufflinks. I am getting the following error: [bam_header_read] EOF marker is absent. The …
cuffmerge error for loading annotation file
written 11.5 years ago by nikhilvgbt •

Hi, I am trying to run cuffmerge but I am getting the following error. Could you please tell me the what the problem is and …
cuffmerge does not give merged.gtf
written 11.8 years ago by Floydian_slip

Hi, I am running cuffmerge to merge a few gtfs that I have created using cufflinks. This is the command I use: cuffmerge -o merged …
cufflink and cuffmerge error
written 12.1 years ago by BDK_compbio

After running cufflink for two samples of RNA-Seq data, I used cuffmerge and executed the following command cuffmerge -p 8 -g <directory>/<gff file> -s <directory>/<refernec …
Struggling With Cufflinks Into Cuffmerge
written 14.7 years ago by Craig Anderson •

<p><strong>Heya, I'm trying to stick RNAseq data through tophat and cufflinks, however, cufflinks doesn't like the accepted_hits.bam (we're on v1.2.0 now, but its still the …
Tophat Question: No Accepted_Hits.Bam Generated
written 15.1 years ago by Rnaer •

<p>I am using tophat to map the SOLiD single-end 50mer reads to S.cerevisae genome. The commands I used are:</p> <pre><code>$ bowtie-build -C reads/sgd_genome.fa reads/sgd_genome $ …