[billstevens]

RAM up to ~32 GB is quite cheap; this week I bought another 8 GB for my workstation, which cost us less than US$ 100 (computer brand memory, I guess you can get it much cheaper). I'd invest a few hundred dollars to get a 8 core 16 GB machine, with that you can do expression analysis quite well, in my opinion (no de novo assembly stuff, however)... Or buy cloud computing time.

Thanks for the advice! I've been looking for a machine that has 8 core, but I couldn't find anything that was commercially available for that (unless it was a MacPro, which was $12000). What kind of PC do you have? Did you just build it yourself?

[arvid]

Thanks for the advice! I've been looking for a machine that has 8 core, but I couldn't find anything that was commercially available for that (unless it was a MacPro, which was $12000). What kind of PC do you have? Did you just build it yourself?

I've sent you a PM.

[arvid]

1. Yes, STAR detects insertions and deletions
2. The minimum intron size is determined by the --scoreDelLmax (=20 by default). If the genomic gap is below that value, it's considered deletion, otherwise - intron. The maximum intron size is approximately determined by winAnchorDistNbins*2^winBinNbits = 9*2^16~600kbases by default, which we think works well for mammalian genomes, but you can increase it at will by increasing --winAnchorDistNbins. There is yet another parameter --winFlankNbins that determines maximum gap for lower confidence introns: winFlankNbins*2^winBinNbits.

Ok, I might try it out. I suppose you can *lower* these settings as well? For e.g. Arabidopsis I'd set something like 3-10k bases for max intron size (3 for lower FDR, 10 for maximum sensitivity) and ~10 bases as minimum intron size... At the moment GSNAP performs better than TopHat with such settings (in my hands at least) - but I'd be interested in trying alternatives.

[alexdobin]

Ok, I might try it out. I suppose you can *lower* these settings as well? For e.g. Arabidopsis I'd set something like 3-10k bases for max intron size (3 for lower FDR, 10 for maximum sensitivity) and ~10 bases as minimum intron size... At the moment GSNAP performs better than TopHat with such settings (in my hands at least) - but I'd be interested in trying alternatives.

You can lower the settings, in your case I would recommend
--scoreDelLmax 10 --winAnchorDistNbins 3 --winBinNbits 12 --winFlankNbins 1
That would give the max intron size for high/low confidence of 12/4kb.

If you decide to try STAR and have any questions/problems please email me at dobin~at~cshl.edu