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Search: Posts Made By: AJenkins
Forum: Bioinformatics 02-02-2015, 09:16 AM
Replies: 8
Views: 8,822
Posted By AJenkins
Hi Jen, I'm not sure if there is a way to...

Hi Jen,

I'm not sure if there is a way to use the log2foldchange for coloring of the data points. You'd definitely have to open it up to see how they define the variables. You may be better off...
Forum: General 01-28-2014, 08:30 AM
Replies: 31
Views: 15,788
Posted By AJenkins
Was your human genome FASTA indexed previously...

Was your human genome FASTA indexed previously using a different version?
Forum: General 01-28-2014, 08:14 AM
Replies: 31
Views: 15,788
Posted By AJenkins
This normally means that the program is trying to...

This normally means that the program is trying to access memory that isn't allocated/isn't allowed. This may be a deeper problem than just memory usage. Could have to do with accessing...
Forum: Bioinformatics 01-09-2014, 12:12 PM
Replies: 4
Views: 1,621
Posted By AJenkins
Using upwards of 600 million reads, I have...

Using upwards of 600 million reads, I have aligned the reads to the reference genome using the Tuxedo suite of programs and using a RABT assembly. This gives me around 10,000 completely unknown...
Forum: General 12-17-2013, 08:04 AM
Replies: 31
Views: 15,788
Posted By AJenkins
Hi, Also, if you use Tophat2 which includes...

Hi,

Also, if you use Tophat2 which includes Bowtie you can use the parameters for whatever read length you may be interested in.
Forum: Bioinformatics 12-05-2013, 07:23 AM
Replies: 8
Views: 8,822
Posted By AJenkins
Hi Jason, I just found the reasoning for why...

Hi Jason,

I just found the reasoning for why cuffdiff doesn't report any p-value less than 0.0001, and it can be found at this website: http://sihua.us/Cufflinks.htm

In short it says: The range...
Forum: Bioinformatics 12-04-2013, 02:08 PM
Replies: 8
Views: 8,822
Posted By AJenkins
Hi Jason, Did you ever find an answer to...

Hi Jason,

Did you ever find an answer to this question? I am having a similar problem with my volcano plots with a "ceiling" of the same as yours and am wondering how to correct for it?

-Adam
Forum: RNA Sequencing 11-20-2013, 01:09 PM
Replies: 5
Views: 2,008
Posted By AJenkins
I have found the culprit of the problem. It...

I have found the culprit of the problem. It seems that the sequencing institute aligned the reads to the genome, which makes us think that they received reads and then aligned them genome. In...
Forum: RNA Sequencing 11-20-2013, 07:33 AM
Replies: 5
Views: 2,008
Posted By AJenkins
dpryan, I just contacted the institute that...

dpryan, I just contacted the institute that aligned the files and the didn't use any splice junction aligned like tophat or PASTA, which I foolishly assumed. As they won't send me the read files as...
Forum: RNA Sequencing 11-20-2013, 07:19 AM
Replies: 5
Views: 2,008
Posted By AJenkins
RNA-seq not showing splice junctions

I have two RNA-seq data sets. When one is run through Cufflinks I see isoforms but when I run the other I see no isoforms, only single exons/transcripts, none with multiple exons. Further...
Forum: Bioinformatics 11-19-2013, 02:52 PM
Replies: 7
Views: 3,539
Posted By AJenkins
I am having this same problem, is there any...

I am having this same problem, is there any reason why?
Forum: Bioinformatics 11-12-2013, 11:37 AM
Replies: 4
Views: 1,621
Posted By AJenkins
Cufflinks novel gene discovery

I have two questions regarding novel gene discovery using Cufflinks:

1.) Does anyone have a good answer for what the appropriate FPKM cutoff value should be during gene discovery using Cufflinks. ...
Forum: RNA Sequencing 11-10-2013, 12:34 PM
Replies: 1
Views: 2,010
Posted By AJenkins
Angry Cufflinks Killed Before Complete

I am attempting a RABT assembly of a genome which contains contigs 2L,2R,3L,3R,X, Y_unplaced and UNKN. Cufflinks inspects bundles for each of the 7 contigs provided from the GTF file but when it...
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