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Search: Posts Made By: dalesan
Forum: Bioinformatics 12-10-2014, 07:13 AM
Replies: 2
Views: 4,396
Posted By dalesan
I can't really give you any guidance other than...

I can't really give you any guidance other than pointing you to a post I spotted on biostars, as I am having the same problem of adjacent loci being lumped together under the same XLOC. Actually, I...
Forum: Bioinformatics 04-22-2014, 04:02 AM
Replies: 26
Views: 11,056
Posted By dalesan
From what I have understood, reads that map to...

From what I have understood, reads that map to multiple locations in the genome can not be reliably used in calculating differential gene expression. This is because there is no biologically...
Forum: Bioinformatics 03-25-2014, 05:27 AM
Replies: 26
Views: 11,056
Posted By dalesan
Smile Updated results and summary

Hello All,

I thought I'd chime in again with some updated results after re-running my DEG analysis using bowtie2 to map reads to both the Arabidopsis transcriptome (1 representative isoform per...
Forum: Bioinformatics 03-19-2014, 04:40 AM
Replies: 26
Views: 11,056
Posted By dalesan
Actually, there was no particular reason that I...

Actually, there was no particular reason that I chose to use bowtie 1. I just read up on the differences between bowtie 1 and 2 now, and it seems like bowtie2 has some nice improvements (affine gaps,...
Forum: Bioinformatics 03-19-2014, 03:56 AM
Replies: 26
Views: 11,056
Posted By dalesan
Results of my comparison of mapping to transcriptome vs genome and DEG

So, I've finally gotten around to comparing the results of my differential gene expression analysis based on mapping to the transcriptome and genome of Arabidopsis.

I used bowtie v 1.0.0 to map...
Forum: Bioinformatics 03-16-2014, 12:19 PM
Replies: 26
Views: 11,056
Posted By dalesan
Excellent points, Brian. I didn't think of it...

Excellent points, Brian. I didn't think of it this way, in terms of the repeatability aspect. In my analysis I've limited the mapping to simply the longest isoform in the annotation. Neverthless, I'm...
Forum: Bioinformatics 03-15-2014, 01:37 AM
Replies: 26
Views: 11,056
Posted By dalesan
Sure thing, sazz. Maybe by the end of next week...

Sure thing, sazz. Maybe by the end of next week I'll have something to share.
Forum: Bioinformatics 02-24-2014, 03:40 PM
Replies: 26
Views: 11,056
Posted By dalesan
Thanks guys for the replies. I appreciate your...

Thanks guys for the replies. I appreciate your input. At this point, I think I'm going to run a test comparison between using the genome vs transcriptome to see how congruent the results are when it...
Forum: Bioinformatics 02-24-2014, 03:19 AM
Replies: 26
Views: 11,056
Posted By dalesan
Question Differential Expression: is it better to map reads to genome or transcriptome?

Hello, hello.

This may be a very naive question, but I haven't been able to find an established answer yet in the literature, nor here (bad search technique, perhaps).

I'm about to embark upon...
Forum: Bioinformatics 05-15-2013, 01:19 AM
Replies: 3
Views: 3,814
Posted By dalesan
Nicrob, you're a genious. Thank you for bring...

Nicrob, you're a genious. Thank you for bring this to my attention!!
Forum: Bioinformatics 05-14-2013, 03:56 AM
Replies: 3
Views: 3,814
Posted By dalesan
Red face Cufflinks performs 0 splicing and promoter tests (Arabidopsis)

Hello SEQAnswers community!

Thank you for this wonderful community here and to those of who you donate your time to checking forum posts and helping those in need.. I'm hoping that someone might...
Forum: Bioinformatics 10-03-2011, 04:45 AM
Replies: 7
Views: 4,023
Posted By dalesan
These are excellent points that you bring up. I...

These are excellent points that you bring up. I am still trying to find out the extent of the services required by our in-house researchers. The majority of the sequencing will be done on eukaryotic...
Forum: Bioinformatics 10-03-2011, 04:29 AM
Replies: 7
Views: 4,023
Posted By dalesan
Sweet, thanks. I had a feeling a similar post was...

Sweet, thanks. I had a feeling a similar post was already out there -- but my crappy searching didn't reveal it. Thanks a bunch!
Forum: Bioinformatics 10-03-2011, 03:37 AM
Replies: 7
Views: 4,023
Posted By dalesan
Question Newbie needing advice on required computing power for small-scale NGS facility

Hello, friendly SEQanswers community :).

Recently, we received a sizeable grant to start up a next-gen sequencing facility. Since I am the only bioinformaticist at my institute (but a biologist by...
Forum: Bioinformatics 04-05-2011, 02:59 AM
Replies: 0
Views: 1,793
Posted By dalesan
Unhappy Editing assembly output of amos?

Hello Everyone,

I hope for the love of god that someone might be able to point me in the right direction.

Essentially, I have been having trouble finding some kind of program that will allow me...
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