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Search: Posts Made By: kalidaemon
Forum: Bioinformatics 04-03-2013, 07:26 AM
Replies: 1
Views: 1,434
Posted By kalidaemon
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...
Forum: Bioinformatics 03-16-2012, 04:34 AM
Replies: 2
Views: 2,709
Posted By kalidaemon
Hi Karel It's possible that the AAAA k-mer that...

Hi Karel
It's possible that the AAAA k-mer that you're seeing at around 21 base pairs are arrested transcripts caused by cyclohexamide treatment. You can check this possibility out by looking at...
Forum: Bioinformatics 03-16-2012, 04:16 AM
Replies: 1
Views: 765
Posted By kalidaemon
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...
Forum: Sample Prep / Library Generation 06-10-2011, 05:59 AM
Replies: 2
Views: 3,124
Posted By kalidaemon
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...
Forum: Sample Prep / Library Generation 06-10-2011, 05:55 AM
Replies: 12
Views: 7,487
Posted By kalidaemon
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...
Forum: RNA Sequencing 05-11-2011, 06:58 AM
Replies: 23
Views: 18,444
Posted By kalidaemon
Thanks. Fixed the memory issue and now running...

Thanks. Fixed the memory issue and now running fine.
Forum: RNA Sequencing 05-10-2011, 04:44 AM
Replies: 23
Views: 18,444
Posted By kalidaemon
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...
Forum: Bioinformatics 11-02-2010, 06:27 AM
Replies: 7
Views: 15,979
Posted By kalidaemon
.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...
Forum: Bioinformatics 10-20-2010, 07:32 AM
Replies: 7
Views: 4,223
Posted By kalidaemon
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...
Forum: Bioinformatics 10-18-2010, 05:33 AM
Replies: 7
Views: 4,223
Posted By kalidaemon
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...
Forum: Bioinformatics 10-18-2010, 05:13 AM
Replies: 11
Views: 8,667
Posted By kalidaemon
I feel your pain with R... I've been using MACS,...

I feel your pain with R... I've been using MACS, which is a software package from Shirley Liu's group: http://liulab.dfci.harvard.edu/MACS to analyze my ChIP-Seq data and have been really happy with...
Forum: Bioinformatics 10-14-2010, 10:52 AM
Replies: 12
Views: 6,479
Posted By kalidaemon
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. ...
Forum: Bioinformatics 10-14-2010, 10:35 AM
Replies: 7
Views: 4,223
Posted By kalidaemon
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...
Forum: Introductions 10-14-2010, 10:19 AM
Replies: 373
Views: 120,278
Posted By kalidaemon
Hi everyone I'm a postdoc in Boston. Working...

Hi everyone
I'm a postdoc in Boston. Working with both ChIP-Seq and RNA-Seq data to understand global differences in estrogen receptor binding and estrogen-mediated gene expression in...
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