Avoid changing the GTF file
I would caution against messing around with the GTF file, as in the future this should break, as soon as Ensembl switches to the next version. In addition, it doesn't work for any other organisms.
I am running cufflinks and solved the problem differently: I indexed the original Ensembl genome, ran bowtie on it, converted the samfile to bam, sorted it, removed this weird transcript from the Ensembl file and ran cufflinks normally, without any awk script.
here is a log file of what I did:
I would caution against messing around with the GTF file, as in the future this should break, as soon as Ensembl switches to the next version. In addition, it doesn't work for any other organisms.
I am running cufflinks and solved the problem differently: I indexed the original Ensembl genome, ran bowtie on it, converted the samfile to bam, sorted it, removed this weird transcript from the Ensembl file and ran cufflinks normally, without any awk script.
here is a log file of what I did:
Code:
bowtie-build -C Mus_musculus.NCBIM37.61.dna.toplevel.fa Mus_musculus.NCBIM37.61.dna.toplevel_c bowtie -f -C -m 1 -p4 --sam $(BOWTIEINDEX) $$i > $(MAPPEDREADS)/`basename $$i .txt`.sam samtools view -Sb sam/SL005_R00002_RME033_01pg_F3.csfasta.sam > sam/SL005_R00002_RME033_01pg_F3.csfasta.bam samtools sort -Sb SL005_R00002_RME033_01pg_F3.csfasta.bam SL005_R00002_RME033_01pg_F3.csfasta.sorted 512391 grep -v ENSMUST00000127664 Mus_musculus.NCBIM37.61.gtf > Mus_musculus.NCBIM37.61.corrected.gtf ~/software/cufflinks-0.9.3/cufflinks -G Mus_musculus.NCBIM37.61.corrected.gtf -v sam.old/SL005_R00002_RME033_01pg_F3.csfasta.sorted.
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