Hello! What do you think would be the ideal sequencing conditions

[Matt Thornton]

Hello!

I am trying to help a collaborator design an experiment to detect fusion proteins using STAR-Fusion and FusionInspector.  Mostly I don't have an opportunity to adjust the sequencing conditions as I get the data after it was generated.  I was thinking it would be better as single-end sequencing and then relatively deep, 30 milllion reads per replicate.

The sequencing providers usually are financially punitive when you deviate from 150PE. It's important so worthwhile to get correct.

Any information or advice is greatly appreciated. Thanks!

Matt

[Brian Haas]

Hi,

150 PE would work well here.  Try running with merged replicates to boost total reads, and then run separately with the individual replicates to examine replicability - or label your read names with the replicate name so you can just examine the bulked run outputs to see which evidence reads correspond to each of the replicates.

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Brian J. Haas
The Broad Institute
http://broadinstitute.org/~bhaas