Dear All,
I have run cufflinks with "-g" (RABT assembly) and "--no-faux-reads" option on a single end, un-stranded sequencing data. As reference I have provided a pooled gtf file comprising of refseq, ensembl and mRNA transcripts. I observed that cufflinks builds many transcripts on the basis of the reference which do not have any read coverage or very less read coverage.
I would like to avoid this situation. I thought using the "--no-faux-reads" solves my problem but it does not. I would like to use the RABT assembly with a reference file but want to disallow cufflinks from building transcripts for which there are no mapped reads.
I have run cufflinks with "-g" (RABT assembly) and "--no-faux-reads" option on a single end, un-stranded sequencing data. As reference I have provided a pooled gtf file comprising of refseq, ensembl and mRNA transcripts. I observed that cufflinks builds many transcripts on the basis of the reference which do not have any read coverage or very less read coverage.
I would like to avoid this situation. I thought using the "--no-faux-reads" solves my problem but it does not. I would like to use the RABT assembly with a reference file but want to disallow cufflinks from building transcripts for which there are no mapped reads.
Comment