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Search: Posts Made By: jdanderson
Forum: Bioinformatics 05-17-2012, 08:51 PM
Replies: 15
Views: 7,753
Posted By jdanderson
Sorry, I actually can't recall how I resolved...

Sorry, I actually can't recall how I resolved this error, although I wasn't using Tophat v2.0 when I ran into it.

Maybe Cole, or another Tophat programmer could be of more help. It also might...
Forum: Bioinformatics 12-29-2011, 03:47 PM
Replies: 1
Views: 2,313
Posted By jdanderson
Bowtie2 in the Tophat/Cufflinks pipeline?

Hey Everyone,

Has anyone tried to plug Bowtie2 output into Cufflinks with success?

It seems as though Tophat may not be able to run on top of Bowtie2, is that accurate? If so, has anyone heard...
Forum: Bioinformatics 08-01-2011, 11:39 AM
Replies: 1
Views: 1,748
Posted By jdanderson
Here is an example of my modified Ensembl .gtf...

Here is an example of my modified Ensembl .gtf file:


Cheers,
Johanthon
Forum: Bioinformatics 08-01-2011, 11:31 AM
Replies: 1
Views: 1,748
Posted By jdanderson
Cuffcompare Class Codes

Hello Everyone,

In my CuffCompare analysis all the class codes in the .tmap file are all "="...."Complete match of intron chain". I used the -r function with a converted Ensembl file. The rest...
Forum: Bioinformatics 08-01-2011, 10:51 AM
Replies: 0
Views: 1,476
Posted By jdanderson
CuffDiff q-value

Hey Everyone,

I have several positive control genes that show up in my CuffDiff analysis with a q-value and p-value of 0.0 . However, they appear to be significantly expressed in my samples (ie...
Forum: Bioinformatics 07-19-2011, 06:02 AM
Replies: 15
Views: 7,753
Posted By jdanderson
Tophat: segment-based junction search failed with err =-11

Hello Everyone,

I was wondering if anyone has ever gotten or knows the source of the following error. I'm running Tophat (v1.3.1) on a dual core, 16GB RAM (older) desktop. The following was my...
Forum: RNA Sequencing 11-03-2010, 04:27 PM
Replies: 15
Views: 12,759
Posted By jdanderson
Hello Zhengz, Thank you for your reply. I...

Hello Zhengz,

Thank you for your reply. I think part of the problem with my approach to this matter is my general lack of statistical savvy. Could you perhaps provide a good starting point or...
Forum: RNA Sequencing 11-03-2010, 04:18 PM
Replies: 6
Views: 7,476
Posted By jdanderson
Hello cjohnson, I am far from an expert on...

Hello cjohnson,

I am far from an expert on this matter, but to get the ball rolling on your thread:

In general, the longer the better and paired ends (especially) are helpful. I think the...
Forum: Bioinformatics 11-03-2010, 03:59 PM
Replies: 31
Views: 15,797
Posted By jdanderson
Hello Everyone, I would like to second...

Hello Everyone,

I would like to second mgogol's suggestion. It is part of a larger set of tools called FASTX Toolkit: http://hannonlab.cshl.edu/fastx_toolkit/index.html

I've found the tools to...
Forum: RNA Sequencing 11-03-2010, 03:51 PM
Replies: 15
Views: 12,759
Posted By jdanderson
Hello all, I am also very interested in...

Hello all,

I am also very interested in everyone thinks about this as well. I've been debating on changing the zeros to ones to get some usable output, especially in cases where the denominator...
Forum: Bioinformatics 10-11-2010, 09:00 PM
Replies: 1
Views: 1,023
Posted By jdanderson
Cuffdiff output question

Hello All,

I was wondering if anyone can tell me why the output files of Cuffdiff (eg gene_exp.diff) have several lines for the exact same chromosomal location?

...
Forum: Bioinformatics 10-11-2010, 08:39 PM
Replies: 8
Views: 6,878
Posted By jdanderson
@Natstreet- Hello Natstreet, I would be very...

@Natstreet- Hello Natstreet,

I would be very interested in reading your protocol for displaying Gbrowse data, as I am not familiar with Gbrowse. If it is at all possible, could you also post any...
Forum: Bioinformatics 10-11-2010, 02:25 PM
Replies: 10
Views: 2,634
Posted By jdanderson
Hello Jet Speeder, Did you ever figure...

Hello Jet Speeder,

Did you ever figure out/resolve this error code? I just received a similar print out.

Thank you for any guidance you might be able to give.

Regards,
Johnathon
Forum: Bioinformatics 10-10-2010, 06:24 PM
Replies: 2
Views: 3,154
Posted By jdanderson
Hello All, Just wondering if anyone could...

Hello All,

Just wondering if anyone could provide some type of feedback on how they are visualizing the Cuffdiff gene and isoform FPKM values? I've written a script to parse and sort the log of...
Forum: Bioinformatics 10-10-2010, 06:16 PM
Replies: 1
Views: 1,994
Posted By jdanderson
Tophat "butterfly" option annomaly

Hello All,

So I reran some of my data with the new Tophat Butterfly option to see how it may of effected the output and I ended up having to stop the run due to the fact that it created an...
Forum: Bioinformatics 10-07-2010, 05:40 PM
Replies: 2
Views: 3,154
Posted By jdanderson
Cuffdiff Visualization

Hello All,

How are some of you visualizing the Cuffdiff output files?

Is it just a matter of parsing (via a script) the FPKM and p-values out of the file and visualizing them in something akin...
Forum: Bioinformatics 10-07-2010, 11:22 AM
Replies: 13
Views: 9,919
Posted By jdanderson
Hello All, Wow, great last couple of posts. ...

Hello All,

Wow, great last couple of posts. I was especially intrigued by the mention of the two databases (which i was not familiar with), very interesting. Sounds like there is a lot of...
Forum: Bioinformatics 10-06-2010, 07:24 PM
Replies: 10
Views: 7,650
Posted By jdanderson
Hello jjw14, Wow, I wish I would have paid...

Hello jjw14,

Wow, I wish I would have paid heed to your advice and tried to use smaller files to test the connection. I uploaded a Solexa 40SR file and it took almost 24 hours. In the meantime I...
Forum: Bioinformatics 10-06-2010, 07:01 PM
Replies: 36
Views: 8,587
Posted By jdanderson
Hello Kevin, I am not sure. I cannot...

Hello Kevin,

I am not sure. I cannot directly tell from the documentation, however, i don't see any mention of color space reads. Maybe you could query the Hannon Lab if you don't get an...
Forum: Bioinformatics 10-05-2010, 12:56 PM
Replies: 10
Views: 7,650
Posted By jdanderson
Hello jjw, Thank you for the reply. I was...

Hello jjw,

Thank you for the reply. I was actually just getting ready to set up an HTTP server from my desktop due to the fact that for this set of samples I have to manipulate the files on my...
Forum: Bioinformatics 10-05-2010, 11:31 AM
Replies: 13
Views: 9,919
Posted By jdanderson
Hello Cliff, Well I guess I figured the...

Hello Cliff,

Well I guess I figured the exonic boundaries would be the de facto splice sites (a script could parse the data for you). As for the promoter, that seems like a tough call. Even if...
Forum: Bioinformatics 10-05-2010, 06:48 AM
Replies: 4
Views: 3,922
Posted By jdanderson
Hello Hypatia, So I just gave the Wilhelm...

Hello Hypatia,

So I just gave the Wilhelm paper (Defining transcribed regions using RNA-seq) a quick look over and it appears that they are talking about the quality filtration that occurs in...
Forum: Bioinformatics 10-04-2010, 08:48 PM
Replies: 10
Views: 7,650
Posted By jdanderson
Hello jjw14, Did you ever find a solution to...

Hello jjw14,

Did you ever find a solution to your problem?

Regards,
Johnathon
Forum: Bioinformatics 10-04-2010, 05:57 PM
Replies: 4
Views: 3,922
Posted By jdanderson
Hello Swarbre and Hypatia, I think...

Hello Swarbre and Hypatia,

I think Bowtie/Tophat may do some quality trimming in its processing, but if you want to have some more control of the quality of reads that pass you can use FASTX...
Forum: Bioinformatics 10-04-2010, 05:43 PM
Replies: 36
Views: 8,587
Posted By jdanderson
Hello All, I am updating my progress in case...

Hello All,

I am updating my progress in case this may help someone in the future.

As previously mentioned I used the FASTX Toolkit on the export.txt and extended.txt files from Illumina...
Showing results 1 to 25 of 45

 


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