Hi,
I've got RNA-Seq data (pe 100bp) from several biological replicates and 11 different conditions and want to compare DE between conditions.
I'm using the tuxedo suite (tophat, cufflinks) and wanted to know if I should run both replicates through tophat at the same time (specified as reps) , and use the output for cufflinks, or separately, and specify them as replicates in cufflinks?
Additionally, the samples have been multiplexed (so each replicate is split over two lanes) - and I've currently merged the multiplexed reads for each replicate - do I lose power by doing this?
Any advice would be great!
Thanks,
N
I've got RNA-Seq data (pe 100bp) from several biological replicates and 11 different conditions and want to compare DE between conditions.
I'm using the tuxedo suite (tophat, cufflinks) and wanted to know if I should run both replicates through tophat at the same time (specified as reps) , and use the output for cufflinks, or separately, and specify them as replicates in cufflinks?
Additionally, the samples have been multiplexed (so each replicate is split over two lanes) - and I've currently merged the multiplexed reads for each replicate - do I lose power by doing this?
Any advice would be great!
Thanks,
N
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