I am a newcomerto the RNAseq field. I have been trying to get (differential) expression values from my experiments (rat and mouse). To achieve this I want to run tophat and cufflinks with annotated transcripts/genes (i.e. -G option in top hat). this requires a GTF or GFF file. I have searched in different sources: iGenomes, Seq_gene.md.gz files from NCBI, refFlat.txt.gz from UCSC and genes.GTF from Ensembl (the latter is missing mitochondrial RNA for instance). however, these either have the wrong file extension, formats and/or the chromosome names do not match.
Does anybody know what currently is the best place to obtain both a reference genome and annotated transcripts/genes (possibly even index files)?
Or are there certain scripts I need to run to convert either my genome fileor my GTF file to the correct format?
the previous post on this seems to be somewhat outdated: http://seqanswers.com/forums/showthread.php?t=12694
Thanks in advance,
Rob
Does anybody know what currently is the best place to obtain both a reference genome and annotated transcripts/genes (possibly even index files)?
Or are there certain scripts I need to run to convert either my genome fileor my GTF file to the correct format?
the previous post on this seems to be somewhat outdated: http://seqanswers.com/forums/showthread.php?t=12694
Thanks in advance,
Rob
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