I am trying to run Cufflinks/cuffmerge/cuffdiff. So far I have aligned my RNAseq reads with STAR using the appropriate options to create a bam file that can be used in cufflinks. I then ran cufflinks with a gff file that I had modified and my bam files, one at a time, like this:
cufflinks -p 8 -G '/home/Mus_musculus.GRCm38.85_Modified.gff3' 'home/STAR_Alignments/Sample1Aligned.sortedByCoord.out.bam'
I did this cufflinks command for each bam file in my sample group.
Then I created a text file with the path to each output file from cufflinks, the transcripts.gtf files. Then tried to run cuffmerge like this:
cuffmerge -p 8 -g '/home/Mus_musculus.GRCm38.85_Modified.gff3' '/home/Cufflinks_Output/6_months/assembly_GTF_list.txt'
And all I can get is this error:
[Sun Sep 11 20:02:16 2016] Beginning transcriptome assembly merge
-------------------------------------------
[Sun Sep 11 20:02:16 2016] Preparing output location ./merged_asm/
[Sun Sep 11 20:02:29 2016] Converting GTF files to SAM
[20:02:29] Loading reference annotation.
GFF Error: duplicate/invalid 'transcript' feature ID=transcript:ENSMUST00000045689
[FAILED]
Error: could not execute gtf_to_sam
Can someone please help. I am not computer suave enough to figure it out on my own.
Thank you in advance.
cufflinks -p 8 -G '/home/Mus_musculus.GRCm38.85_Modified.gff3' 'home/STAR_Alignments/Sample1Aligned.sortedByCoord.out.bam'
I did this cufflinks command for each bam file in my sample group.
Then I created a text file with the path to each output file from cufflinks, the transcripts.gtf files. Then tried to run cuffmerge like this:
cuffmerge -p 8 -g '/home/Mus_musculus.GRCm38.85_Modified.gff3' '/home/Cufflinks_Output/6_months/assembly_GTF_list.txt'
And all I can get is this error:
[Sun Sep 11 20:02:16 2016] Beginning transcriptome assembly merge
-------------------------------------------
[Sun Sep 11 20:02:16 2016] Preparing output location ./merged_asm/
[Sun Sep 11 20:02:29 2016] Converting GTF files to SAM
[20:02:29] Loading reference annotation.
GFF Error: duplicate/invalid 'transcript' feature ID=transcript:ENSMUST00000045689
[FAILED]
Error: could not execute gtf_to_sam
Can someone please help. I am not computer suave enough to figure it out on my own.
Thank you in advance.
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