cufflinks GTF files incompatible with cuffmerge?

Hello all..

I was trying to merge cufflink generated GTF file using Cuffmerge into single merged.gtf file but didn't succeeded. Running the script gave following error:

(base) [ska112@login002 cufflinks-2.2.1.Linux_x86_64]$ cuffmerge -o cuffmerge_new -g Bombyx.gtf -s bombyx.fa assmeblies.txt 

[Wed Jun 24 17:34:43 2020] Beginning transcriptome assembly merge
-------------------------------------------

[Wed Jun 24 17:34:43 2020] Preparing output location cuffmerge_new/
[Wed Jun 24 17:34:45 2020] Converting GTF files to SAM
[17:34:45] Loading reference annotation.
GFF Error: duplicate/invalid 'transcript' feature ID=BGIBMGA005056-RA
        [FAILED]
Error: could not execute gtf_to_sam

rna-seq

• 781 views • link

updated 6.1 years ago by Ram

• written 6.1 years ago by sahilbioinf0 •

0 answers

No answers yet.

More posts like this

tophat2 runs with error:: segment-based junction search failed with err =-6
written 4.0 years ago by pxd •

The command I use is : tophat -p 8 -r 101 -G gencode.v41.annotation.gtf -o GM12878_1 pxd ENCFF001REJ.fastq ENCFF001REK.fastq [2022-08-18 17:30:19] Beginning TopHat run (v2.1.1) ----------------------------------------------- …
Cuffmerge Error: Converting GTF files to SAM
written 5.5 years ago by sahar.salimi92 •

Hi, I run `cuffmerge -g hg38_refseq.gtf -s chrX.fa -p 8 assemblies.txt` command but I get the following error [Wed Feb 24 22:07:24 2021] Beginning transcriptome …
Cuffmerge error when merging transcript.gtf files
written 5.7 years ago by sarai •

Hi everyone! I'm new on RNA-Seq analysis and I need your help. I'm trying to merge the transcript.gtf files I got with cufflinks but when …
The Tophta2 ERR, [ERRno 2]
written 6.5 years ago by ynau_kanghuadu •

Now, I sued the Tophat2 (V2.1.1) work, my software can run normally, but cant get *.hit.bam. and I've run the software many time and it's …
i meet an error when i run the cuffmerge
written 8.5 years ago by 1165576001 •

I used tophat, cufflinks to analyse clean reads of RNA-seq, and get the transcriptome expression profile of my samples. annotation.gtf and genome.fa I used in …
error in cuffmerge
written 9.1 years ago by mra8187 •

Dear all i am using cuffmerge and get this error ; what can i do ? my script is : cuffmerge -p 4 -o '/home/mra/Desktop/ensan/merge-out' …
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 …
tophat error help
written 10.4 years ago by clizama •

I was running tophat using galaxy in amazon cloud and I git this error, someone can help me to fix it. ``` [2016-03-24 07:39:10] Checking …
Cufferge IOError: Errno 2 no such file or directory
written 10.6 years ago by Yuka Takemon •

Hello, The following is my script: ``` #!/bin/bash -l #PBS -l nodes=1:ppn=20,walltime=24:00:00 module load cufflinks/2.2.1 ##define directories and other variables #directory to input cufflinks dir_cufflinks=/pathto/Annotation/cufflinks_preqc …
Problem using a custom blast database in tblastx
written 12.1 years ago by arronar

Hello. I tried to create a custom DB for blast. I downloaded fasta files from NCBI from an SRA project and then run this command …