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Old 08-19-2014, 04:43 AM   #1
M@rc0
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Default Laptop RNASeq Analysis

Hi everybody,
After my Lab bought a Miseq I'm about to enter to the world of bioinformatics. Iím aware I canít do all types of analysis in a laptop, but I mean to work at home or when Iím out of town..... Is the configuration written below good or is it too powerful and useless ( and too expensive O.o)?
I think I'll use Bio-Linux and I'll focus on Rna Seq.
Thank you in advance.


SANTECH N87
CPU: Intel Core i7-4910MQ 2.90 GHz (QC, 8MB, T 3.90 GHz)
- RAM: 16 GB DDR3L 1.600MHz CL9 (2x8.192MB)
- SSD 1.0TB Samsung 840 EVO (S.ATA III)
- Display: 15,6" LED FullHD 1.920x1.080 NO-Glare
- NVIDIA GeForce GTX 870M 6,0GB GDDR5
- Unitŗ Ottica: Blu-ray 6X (BD-R/DVD+/-RW/CD-RW)
- Wireless: Intel Centrino Advanced-N 6235 (300Mbps, a/b/g/n + Bluetooth 4.0)
nearly 2000 euro
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Old 08-19-2014, 04:50 AM   #2
dpryan
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Are you including alignment as well and what organism do you study? It's often better to just use a larger server and just connect to it remotely. If you do plan to do the alignment yourself, you may need more RAM if you want to use STAR (otherwise, you'll be stuck with slower tools like tophat2).
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Old 08-19-2014, 05:54 AM   #3
M@rc0
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You are right sorry, the organism is Homo Sapiens and for the alignment I was thinking to do it by myself but as you said it should be better working in cloud.... I'm a beginner in this field so my ideas are not always right...
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Old 08-19-2014, 06:08 AM   #4
GenoMax
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Even if it does work on the laptop, the question is should you do it that way. If you are going to work with human data then save yourself some trouble and don't invest your money in that expensive laptop. You would be better off doing the analysis elsewhere as Devon has already suggested. If you truly want portability then there are mobile workstation class laptops that can have significantly more RAM but they are going to be much more expensive.

BTW: What are you planning to do on a MiSeq with human samples? Targeted re-sequencing/exome capture?

Last edited by GenoMax; 08-19-2014 at 06:11 AM.
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Old 08-19-2014, 06:20 AM   #5
M@rc0
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Ok, perfect..also for my money ..... About the applications, I was thinking about targeted resequencing, profiling coding trascriptome and miRNA...... Is it ok for a MiSeq?
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Old 08-19-2014, 08:19 AM   #6
GenoMax
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All those applications would be fine as long as you take into account the expected data output from MiSeq and adjust for the level of coverage you would need for a question under consideration.
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Old 08-19-2014, 09:19 AM   #7
M@rc0
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Perfect about the laptop, I can reduce the ram, cpu and it should befine .... is it right?
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Old 08-19-2014, 09:43 AM   #8
GenoMax
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Stick with 16G RAM, if you can, but 8G would be adequate for normal use (if that saves you significant cash). Unless you intend to play graphics-intensive games on this machine the current video card is an overkill and may become a drain on the battery.

Last edited by GenoMax; 08-19-2014 at 09:47 AM.
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Old 08-19-2014, 06:50 PM   #9
biocomputer
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I use both my laptop and a cloud computing system for analysis. Most alignment is done on the cloud because aligning is more resource intensive. Also, an alignment could take several hours or more and if you're running it locally you can't turn off your computer until it's done, which can get pretty inconvenient at the end of the day when I want to turn off my laptop and take it home from the lab. The cloud will also let you cue up many things at once.

I think a 1TB SSD is overkill. Instead, I would look for a laptop that has room for multiple hard drives. For example, I have a 256GB mSATA SSD and 2x1TB HDD's (I replaced the optical bay to add the 2nd HDD). SSD for OS and program files and HDD's for all my big sequencing data. Note that mSATA has largely been replaced by various types of M.2 SSD's. You should also factor in some sort of backup system for your files (eg. external hard drives).

Another benefit would be a laptop that can support multiple monitors, most laptops can support one external but not as many can support more than that. I use my laptop screen plus two externals. I've only used Ubuntu but had a bit of trouble with externals, so make sure whatever GPU you get has good drivers for the OS you'll be using.

If you end up using a cloud computing system for the more intensive work like aligning, you could probably go with a slightly cheaper CPU but I'd stick with a current generation 4 core/8 thread i7, I have a 2nd generation 4-core i7 and it's still good enough after 2 years for the stuff I do locally (though something a little faster would be nice sometimes). I would keep the 16GB of RAM.

Last edited by biocomputer; 08-19-2014 at 06:58 PM.
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Old 08-20-2014, 12:12 AM   #10
M@rc0
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Wow, nice tips=) thanks to everybody...very interesting your considerations about the hdd
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Old 10-25-2016, 10:05 PM   #11
Hiran
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I agree with Dr. Guarracino and will be more focused in the hardware specifications rather than the brand itself. If you are going to do RNAseq analysis the first question would be: Do you have a reference (for example Arabidopsis or rice) or do you need to do a de-novo assembly ? How much data do you have ? What tools do you want to use ? Do you have any previous knowledge of Linux and command line tools ? Here some orientation.he short answer is yes, it will run RNA-Seq analysis on most model organisms. The longer answer is you'll still always get much better performance with more cores and with Xeon workstation/server CPUs (even at lower clock speeds), so if you are planning on doing lots of RNA-seq analysis a good workstation or shared server is a very good investment for a lab. But the laptop will do if you aren't doing much. Keep in mind that to do it in a reasonable amount of time the laptop will be pretty much just doing the RNA-Seq so you may find it difficult to also do any other work on it while the analysis is running. And depending on the software tools and size of your dataset some of the steps may take long enough that you'll need to leave it running overnight. Just some things to keep in mind.
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Last edited by GenoMax; 10-26-2016 at 04:02 AM.
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