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Old 06-27-2013, 12:08 PM   #1
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Location: USA

Join Date: Feb 2012
Posts: 7
Default Cuffmerge: merging reference and transcript GTFs?

Dear All.

After running cufflinks

cufflinks -p 10 --frag-len-mean 400 --frag-len-std-dev 100 -N --GTF-guide ${gtf} --frag-bias-correct ${fasta} --multi-read-correct -o cufflinks_all all.accepted_hits.bam
I got a 12M transcripts.gtf file that I eventually merged with a 240M reference GTF file using cuffmerge:

cuffmerge -p 10 -o cuffmerge_all --ref-gtf ${gtf} --ref-sequence ${fasta} assemblies.txt
(on assemblies.txt there is only the transcripts.gtf produced previously by cufflinks)

Yet, cuffmerge outputs a 142M merged.gtf. Assuming that cuffmerge makes a non-redudant union of the transcripts and reference GTF files, shouldn't merged.gtf weight at least as the reference GTF (240M)?

Thanks in advance
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