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Forum: Bioinformatics 09-07-2012, 11:43 AM
Replies: 5
Views: 1,971
Posted By thedavid
Well. LifeScope is a real PITA to install. We...

Well. LifeScope is a real PITA to install. We have a nice SGE-based cluster here and support staff to install software for us. Unfortunately LifeScope appears to need it's own computer to run a...
Forum: Bioinformatics 08-28-2012, 08:22 AM
Replies: 5
Views: 1,971
Posted By thedavid
Thank mbblack. It looks like it's best to use...

Thank mbblack. It looks like it's best to use ABI's mapper.

So, what's a recommended tool to convert from colorspace to basespace after mapping? I can't figure out if ABI provides one.
Forum: Bioinformatics 08-27-2012, 01:28 PM
Replies: 5
Views: 1,971
Posted By thedavid
Recommendations for RNA-seq mapping for ABI/Illumina data-sets

I'm trying to compare transcriptomes of developing zebrafish and have tracked down RNA-seq data-sets for several of the time-points I'm interested in.

The problem is that there are three different...
Forum: Bioinformatics 07-26-2012, 02:25 PM
Replies: 16
Views: 2,322
Posted By thedavid
Sorry, first let me start off by saying it's...

Sorry, first let me start off by saying it's possible I've totally mis-understood your issue.
Second, if you fail to deal with the strand of your features (ie is the gene on the positive or negative...
Forum: Bioinformatics 07-26-2012, 02:12 PM
Replies: 16
Views: 2,322
Posted By thedavid
Is it a strand issue? I've made that mistake...

Is it a strand issue? I've made that mistake before......
Forum: Bioinformatics 07-26-2012, 02:11 PM
Replies: 2
Views: 4,293
Posted By thedavid
Get peaks from your bed files (macs14 or...

Get peaks from your bed files (macs14 or macs2)......intersectBed (to find the overlapping peaks)....output to a text file.....import into R.....run your correlation coefficient on the scores (from...
Forum: Bioinformatics 07-20-2012, 09:05 AM
Replies: 4
Views: 3,356
Posted By thedavid
UCSC genome browser -> genome of choice (hg18 or...

UCSC genome browser -> genome of choice (hg18 or hg19) -> Tables -> Groups(Genes...) -> Track (RefSeq)

When you output you have the option of selecting the format (bed) and can pick whether you...
Forum: Literature Watch 04-09-2012, 08:45 AM
Replies: 19
Views: 11,659
Posted By thedavid
1. Thanks, I'll give it a try. 2. Sorry, I...

1. Thanks, I'll give it a try.
2. Sorry, I wasn't clear - if the Klenow was added, then 10 mM dNTPs were added. What I meant was that 100 uM dNTPs were added instead of 100 uM T-mix. As a control,...
Forum: Literature Watch 04-06-2012, 12:45 PM
Replies: 19
Views: 11,659
Posted By thedavid
Has anyone not in Hinrich Gronemeyer's lab gotten...

Has anyone not in Hinrich Gronemeyer's lab gotten this process to work? I've been trying for well over a month to get it working. After a tremendous amount of troubleshooting I've made a few...
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