[BioC] Problems easyRNASeq

[Yates, Steven A]

Dear Sir/Madam

I am in the process of learning how to use the easyRNAseq package for
bioconductor but have a question/problem. The problem is that the
organisms I am working with do not have any comprehensive genome
information (or any prior sequencing) in effect I will be creating a de
novo transcriptome. Therefore there is no annotation file available for
me to use, all I have is a list of transcripts. How will this work for
this package? I am quite happy for the results to be reads per
transcript etc, is it neccessary to create an annotation file (gff) for
this purpose or not. I have created a gtf file using cufflinks, which should be ok?  #

The second problem I am encountering is the chrSizes. How do I get around the chromosome sizes problem???, if you have any advice it would be appreciated

many thanks

Steven Yates