Hello genome browsers, Does anyone know how to filter rRNA out of a GTF file?
I would also really like to know how to obtain a GTF file with only rRNA. What I really need is a complete list of gene ids - like the ones that appear in the GTF file that correspond to rRNA. For a class project, I am using RSEM to map and count reads per gene with multiple RNA-seq datasets and then comparing differential expression results between DESeq and EdgeR. I believe that the rRNA and possibly the mtDNA genes are negatively affecting my gene expression results due to excessive coverage. I basically want to filter my RSEM results to exclude genes with IDs that correspond to rRNA. By the way, RSEM uses Bowtie to prepare a transcriptome reference sequence and map reads. To prepare the transcriptome reference sequence, one must input the GTF file along with the entire human genome. I am pretty sure that I can figure out how to filter the mtDNA genes as that just requires filtering out an entire chromosome. Thanks for your time. Sincerely, Clayton _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
