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Forum: Bioinformatics 05-08-2010, 06:06 AM
Replies: 1
Views: 1,811
Posted By alperyilmaz
Unhappy USeq - FilterDuplicateAlignments - SAM

I am trying to use USeq for ChIP-Seq analysis. I wanted to run FilterDuplicateAlignments just in case there is potential amplification bias in the sample. Guess what, formatting(1) problem!!

I...
Forum: RNA Sequencing 05-05-2010, 10:00 AM
Replies: 0
Views: 1,790
Posted By alperyilmaz
RNA-Seq biology

As far as I can see the literature is using total RNA for RNA-Seq analysis. This is fine if you're doing gene expression level. But there are numerous studies regarding alternative splicing events. ...
Forum: Wiki Discussion 04-28-2010, 01:07 PM
Replies: 1
Views: 12,649
Posted By alperyilmaz
output format content & tag mayhem

(Eric already got this question and wanted me to post it here as well)

1. Currently, when people click on a output format, they see an empty page (at least the ones i checked). I think it will be...
Forum: Bioinformatics 02-09-2010, 02:25 PM
Replies: 0
Views: 2,140
Posted By alperyilmaz
RNA-Seq cutoff formula..

Hi,

I posted similar question under RNA sequencing, but after second thought Bioinformatics section might be better suited.

After calculating RPMK values for transcripts, how do I calculate the...
Forum: RNA Sequencing 02-08-2010, 04:01 AM
Replies: 1
Views: 1,824
Posted By alperyilmaz
threshold

In Mortazavi et al (Nature Methods,2008. 5: 621) they used 5 RPMK as threshold and reported genes that had RPMK more than 5.0.
Is this applicable to other experiments or this threshold can be...
Forum: Epigenetics 11-18-2009, 09:54 AM
Replies: 20
Views: 63,353
Posted By alperyilmaz
comparisons

Where can I find the results that Nix suggested earlier, same sample sequences tested with different peak finding software?
Forum: Bioinformatics 02-19-2009, 07:24 AM
Replies: 2
Views: 3,274
Posted By alperyilmaz
We're not using GAPipeline. We receive Solexa...

We're not using GAPipeline. We receive Solexa reads in numeric format and do the alignment ourselves with SeqMap.
I don't know what type of Solexa machine is used in our sequencing facility or their...
Forum: Bioinformatics 02-14-2009, 02:31 AM
Replies: 7
Views: 2,473
Posted By alperyilmaz
Hi Anthony, thanks for offering help. one of...

Hi Anthony,

thanks for offering help. one of the IGB developers agreed to fix the issue. So it will be fixed soon.
Forum: Bioinformatics 02-13-2009, 06:42 AM
Replies: 7
Views: 2,473
Posted By alperyilmaz
view .wig files

I was trying to view the resulting .wig files generated by FindPeaks3 in IGB (Genoviz at SourceForge) but there's a problem with IGB and cannot parse .wig file correctly. Is there any other...
Forum: Bioinformatics 02-11-2009, 10:07 AM
Replies: 2
Views: 3,274
Posted By alperyilmaz
Eland output from SeqMap

SeqMap is able to generate Eland output but there are some columns missing in Eland output. Anybody having this problem too?
Forum: Bioinformatics 02-11-2009, 10:00 AM
Replies: 57
Views: 38,345
Posted By alperyilmaz
R package from BioConductor

There's another R package to be released, which will be available thru BioConductor. It's mentioned in a recent workshop. The workshop material can be viewed here...
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