Forum: Bioinformatics
04-03-2013, 08:26 AM
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Replies: 1
Views: 1,646
Hi Nazeen
There's no "best" program or method...
Hi Nazeen
There's no "best" program or method for phylogenetic analysis. It all depends on your data-set, the questions you're asking, and your proficiency with different computer languages. There...
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Forum: Bioinformatics
03-16-2012, 05:34 AM
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Replies: 2
Views: 3,031
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Forum: Bioinformatics
03-16-2012, 05:16 AM
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Replies: 1
Views: 968
Storm help
Hi everyone
I've been running some transcription factor binding site analysis using the Storm and Motifclass utilities in the CREAD package. I got some interesting results using a functional depth...
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Forum: Sample Prep / Library Generation
06-10-2011, 06:59 AM
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Replies: 2
Views: 3,476
I'm doing the same thing and have been able to...
I'm doing the same thing and have been able to increase my yield using phenol/chloroform extraction with phase-lock gels to clean up my ChIPped DNA after reverse cross-linking. Also, you might want...
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Forum: Sample Prep / Library Generation
06-10-2011, 06:55 AM
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Replies: 12
Views: 8,185
Hi Spudybudy
I'm having the same problem, but...
Hi Spudybudy
I'm having the same problem, but not sure whether it's a quantitation, sample abundance, or some other issue. I quantitate my DNA using the Invitrogen Quant-It kit and use 5ng in my...
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Forum: RNA Sequencing
05-11-2011, 07:58 AM
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Replies: 23
Views: 21,023
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Forum: RNA Sequencing
05-10-2011, 05:44 AM
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Replies: 23
Views: 21,023
Seqmonk bug?
I'm also trying to visualize/correct for potential 3' bias in my RNA-Seq data-set and want to try Seqmonk. The problem is that I can't get it to run off my PC which has a Windows XP operating...
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Forum: Bioinformatics
11-02-2010, 07:27 AM
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Replies: 7
Views: 17,385
.bam to .wig conversion
I'm trying do some sanity checks by putting my TopHat output on the UCSC browser. In order to do this, I need to convert my accepted_hits.bam files to .wig files. Has anyone tried to do this? I...
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Forum: Bioinformatics
10-20-2010, 08:32 AM
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Replies: 7
Views: 4,589
fkuo: Thanks! I tried running cuffcompare with...
fkuo: Thanks! I tried running cuffcompare with the -s option and was able to generate a p_id. Unfortunately, my troubles didn't stop there. My combined.gtf file contained tss and p ids that didn't...
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Forum: Bioinformatics
10-18-2010, 06:33 AM
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Replies: 7
Views: 4,589
Thanks! I tried using the .gtf file from...
Thanks! I tried using the .gtf file from cuffcompare as my reference gtf for cuffdiff as you suggested. This solved some problems, but created others. The isoforms, promoters, splicing, and tss...
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Forum: Bioinformatics
10-18-2010, 06:13 AM
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Replies: 11
Views: 9,300
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Forum: Bioinformatics
10-14-2010, 11:52 AM
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Replies: 12
Views: 7,054
Hi Sherry
I had a similar problem which I...
Hi Sherry
I had a similar problem which I solved by downloaded the pre-compiled executable software (cufflinks-0.9.1.Linux_x86_64) and following the (much simpler) install directions in the manual. ...
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Forum: Bioinformatics
10-14-2010, 11:35 AM
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Replies: 7
Views: 4,589
GTF file for cuffdiff 0.9.1
The GTF file I'm using to run cuffdiff has transcript IDs but no p_ids. Consequently, cuffdiff is unable to make the cds, promoters, splicing, and tss_groups files. Is there a database where I...
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Forum: Introductions
10-14-2010, 11:19 AM
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Replies: 373
Views: 148,892
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