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Old 12-06-2010, 11:47 AM   #1
rnaseq
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Location: washington

Join Date: Dec 2009
Posts: 7
Default bacterial RNA-seq workbench options?

Hi all,

I'm working with Illumina RNA-seq data for bacterial samples. I am researching commercial packages for downstream analyses such as identification of DE genes etc. Ideally I would prefer a package that allows me to upload data as fastq files. I can provide the reference genomes for alignments.

The packages I found include CLC bio, Avadis, Partek and Geospiza. I was wondering if any of you can recommend one over the other from your experience (I'm open to other options outside those I listed above). I am a biologist with minimal bioinformatics expertise. Our collaborator has previously used Geospiza and their tech-support ceases to exist a few weeks after purchasing their licence. I'm hoping we can avoid a similar experience by going with a tried and tested recommendation.

Thanks for any leads.
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