I have some yeast RNAseq data and I would like to run RNA-SeQC to get an overview of the quality of the run.
I got both the reference fasta sequence and the GTF file from Ensembl here:
# fasta ftp://ftp.ensembl.org/pub/current_fasta/saccharomyces_cerevisiae/dna/Saccharomyces_cerevisiae.R64-1-1.dna.toplevel.fa.gz # gtf ftp://ftp.ensembl.org/pub/current_gtf/saccharomyces_cerevisiae/Saccharomyces_cerevisiae.R64-1-1.86.gtf.gz
However, it seems that there is no rRNA information in the GTF file. When I run RNA-SeQC, I get the following output in my log:
RNA-SeQC v188.8.131.52 07/11/14 Creating rRNA Interval List based on given GTF annotations Retriving contig names from reference contig names in reference: 17 Loading GTF for Read Counting Converting to refGene Transcript objects to RefGen format: 0 s java.lang.RuntimeException: No rRNA found in GTF transcript_type field at org.broadinstitute.cga.rnaseq.TranscriptList.toRRNAIntervalList(TranscriptList.java:414) at org.broadinstitute.cga.rnaseq.RNASeqMetrics.createRefGeneAndRRNAFiles(RNASeqMetrics.java:1306) at org.broadinstitute.cga.rnaseq.RNASeqMetrics.prepareFiles(RNASeqMetrics.java:196) at org.broadinstitute.cga.rnaseq.RNASeqMetrics.execute(RNASeqMetrics.java:170) at org.broadinstitute.cga.rnaseq.RNASeqMetrics.main(RNASeqMetrics.java:139) No information for rRNA available. Continuing without rRNA calculations. (Using the -BWArRNA flag for best results) ...
I would like the rRNA information if possible. Does anyone know where to get a GTF file with rRNA information for yeast?