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Old 02-13-2015, 07:26 AM   #10
arash82
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Location: Sweden

Join Date: Oct 2014
Posts: 11
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Dear Brian,

Thanks for the extensive response and clarification on how the program works. Very much appreceated.

I kind of forgot to mention that I am using it on RNA-seq data from a HiSeq 2500. I currently don't have access to the mapped file, but I'll try it on them as soon as I can.

The thing is I am using the program (right now at least) just to determine if I am sequencing deep enough or if I can multiplex furthere. I don't need a perfect curve, just an estimate. Was thinking maybe to trim and then run, but shouldn't gain much from that...

Thanks,
Arash

PS. Was also thinking that the spikes are nice in a way as a quility indiciation. I have instances of much higher spikes in my data.
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