Hello,
I am analyzing some bacterial RNA-seq data with cufflinks. Since in bacterial RNA-seq, splicing isn't an issue, I am using a mapping program that does not take splicing into account. I just wanted to get FPKM's for my genes and do some differential expression even though I am aware that cufflinks was created for euk RNA-seq. In the FAQ's, it states that cufflinks will work with bacterial RNA-seq given that I map with a fasta file of already annotated genes. I know cufflinks assembles transcripts, but when I feed it my sam file (generated from mapping program perM by mapping reads to a mulitfasta file of genes in the genome), cufflinks returns multiple locations of one gene in separate rows with all of their own FPKM's. I wanted just an FPKM for each gene. Does anyone have any way to resolve this issue? Cheers.
I am analyzing some bacterial RNA-seq data with cufflinks. Since in bacterial RNA-seq, splicing isn't an issue, I am using a mapping program that does not take splicing into account. I just wanted to get FPKM's for my genes and do some differential expression even though I am aware that cufflinks was created for euk RNA-seq. In the FAQ's, it states that cufflinks will work with bacterial RNA-seq given that I map with a fasta file of already annotated genes. I know cufflinks assembles transcripts, but when I feed it my sam file (generated from mapping program perM by mapping reads to a mulitfasta file of genes in the genome), cufflinks returns multiple locations of one gene in separate rows with all of their own FPKM's. I wanted just an FPKM for each gene. Does anyone have any way to resolve this issue? Cheers.
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