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Old 03-02-2016, 09:45 PM   #1
Location: Vienna

Join Date: Jan 2016
Posts: 10
Default Assigning reads to genes in the absence of genomic annotation

I'm looking for a method to calculate read counts from SAM/BAM files that does not require an annotation file (GTF or BED files).

I've done a de novo transcriptome assembly of an organism which does not have an annotated genome. While there is an available genome for a closely related species, it has not been annotated.

Which program(s) can be used to output count data to a text file suitable for differential expression analysis with DESeq?

If I blastx my transcriptome against uniref 50 (or uniprot_sprot, I'm not sure which database is ideal - but that is another post all in itself) how can this output be integrated with the count data set (either in DESeq or prior to that)?
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