Forum: Bioinformatics
01-07-2015, 02:49 PM
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Replies: 17
Views: 3,380
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Forum: General
11-13-2014, 10:18 PM
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Replies: 3
Views: 2,159
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Forum: General
11-11-2014, 02:20 PM
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Replies: 3
Views: 2,159
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Forum: RNA Sequencing
11-07-2014, 09:25 AM
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Replies: 2
Views: 1,270
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Forum: Sample Prep / Library Generation
11-07-2014, 09:18 AM
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Replies: 5
Views: 1,951
Your input has a lot of really big chromatin...
Your input has a lot of really big chromatin fragments in it still (7-17, 9-14) or its very short with a odd curve shape overall (8-14). It would seem you still need to optimize the sheering and...
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Forum: Sample Prep / Library Generation
11-06-2014, 12:58 PM
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Replies: 5
Views: 1,951
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Forum: Bioinformatics
10-15-2014, 08:47 AM
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Replies: 8
Views: 2,802
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Forum: Bioinformatics
10-15-2014, 08:43 AM
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Replies: 8
Views: 2,802
A small cluster with at least one high memory...
A small cluster with at least one high memory node is probably what would be most efficient if you’re talking about whole department with very different tasks.
If it were me I’d maybe look at...
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Forum: Bioinformatics
10-09-2014, 09:30 AM
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Replies: 20
Views: 9,340
I second GenoMax, if you’re not particularly...
I second GenoMax, if you’re not particularly computationally inclined, managing your own workstation is maybe more than you should try to do.
Often what is possible is that you buy a computer (it...
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Forum: Bioinformatics
10-08-2014, 03:58 PM
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Replies: 6
Views: 1,287
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Forum: Bioinformatics
09-04-2014, 12:23 PM
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Replies: 18
Views: 5,651
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Forum: Bioinformatics
09-04-2014, 09:52 AM
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Replies: 18
Views: 5,651
One other quick suggestion, Supermicro...
One other quick suggestion, Supermicro motherboards and cases are really nice. That case you have picked out looks pretty slick, but it will probably get cramped with a duel LGA 2011 motherboard and...
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Forum: Bioinformatics
09-04-2014, 09:28 AM
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Replies: 18
Views: 5,651
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Forum: Bioinformatics
08-28-2014, 11:08 AM
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Replies: 22
Views: 5,038
I have to agree, don’t go with some...
I have to agree, don’t go with some 'pre-packaged’ commercial software and don’t buy a workstation from them. You’ll get ripped off on the hardware and the software from those places tends to be...
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Forum: Bioinformatics
08-20-2014, 04:11 PM
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Replies: 14
Views: 5,472
since htseq is always going to be in the same...
since htseq is always going to be in the same order, I just use paste (which can takes a space seperated list of your files) and awk. Paste will print the row names for each file, so that's what awk...
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Forum: Bioinformatics
08-18-2014, 03:23 PM
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Replies: 4
Views: 2,985
It sounds messy to me to have 5 wiggles (or 10)...
It sounds messy to me to have 5 wiggles (or 10) overlaid. In my experience this is hard to interpret. I would personally just average the wiggle files and have test and control tracks separated. Its...
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Forum: Bioinformatics
08-13-2014, 05:07 PM
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Replies: 3
Views: 3,075
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Forum: Sample Prep / Library Generation
07-24-2014, 08:20 AM
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Replies: 4
Views: 1,797
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Forum: Bioinformatics
07-22-2014, 08:45 AM
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Replies: 14
Views: 2,852
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Forum: Bioinformatics
07-22-2014, 08:31 AM
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Replies: 9
Views: 1,622
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Forum: Bioinformatics
07-21-2014, 02:06 PM
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Replies: 8
Views: 6,052
Are you trying to compile it from source and...
Are you trying to compile it from source and getting errors or are you just trying the provided binaries and they aren’t working?
If you’re trying to compile it, I’d suggest you try the binaries...
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Forum: Bioinformatics
07-18-2014, 08:35 AM
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Replies: 1
Views: 1,635
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Forum: Bioinformatics
07-16-2014, 11:44 AM
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Replies: 2
Views: 1,127
If you ran maker on just the contigs of your...
If you ran maker on just the contigs of your genome assembly and now you have scaffolds, you should rerun maker from the beginning on those scaffolds. Trying some sort of liftover of your gff file is...
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Forum: Bioinformatics
07-11-2014, 11:52 AM
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Replies: 6
Views: 1,794
The basic idea here is you’re looking for genes...
The basic idea here is you’re looking for genes in which the beta term in the equation expression = beta * stage + constant is significantly different from zero. This is a generalized linear model. ...
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Forum: RNA Sequencing
07-07-2014, 10:14 PM
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Replies: 2
Views: 1,506
Is this RT-qPCR on the same RNA that was...
Is this RT-qPCR on the same RNA that was sequenced?
What was the ct-value for the gene?
How many reads did get for this sample?
There is going to be a pretty big difference between...
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