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Forum: Bioinformatics 05-26-2015, 06:26 AM
Replies: 15
Views: 5,046
Posted By r_sitaram
Hello ersgupta, we were finally able to solve it...

Hello ersgupta, we were finally able to solve it by trying to edit the code and modifying the array size to accommodate the large genome size that we were dealing with. If I remember correctly, our...
Forum: Bioinformatics 11-07-2013, 01:48 AM
Replies: 15
Views: 5,046
Posted By r_sitaram
Hi sagarutturkar, So I tried training GlimmerHMM...

Hi sagarutturkar, So I tried training GlimmerHMM and follow your lead and arrived at the same error 69. I found that atleast in my case, the score.c script was not functioning and I kept getting...
Forum: RNA Sequencing 05-21-2012, 04:15 AM
Replies: 10
Views: 4,190
Posted By r_sitaram
I forgot to mention the p values for those 5...

I forgot to mention the p values for those 5 genes. They are as follows.
ENSRNOG00000005330 E035 0.000108786
ENSRNOG00000009864 E005 0.000152295
ENSRNOG00000017466 E016 0.000166557...
Forum: RNA Sequencing 05-21-2012, 04:12 AM
Replies: 10
Views: 4,190
Posted By r_sitaram
Hello Simon, This is the third...

Hello Simon,
This is the third best gene available. I checked the top 5 and I see this behaviour very distinct only in 2 of them. Iím attaching the pdf of that for your reference. The...
Forum: RNA Sequencing 05-18-2012, 02:10 AM
Replies: 10
Views: 4,190
Posted By r_sitaram
Hello Simon. I'm not sure if you received my...

Hello Simon. I'm not sure if you received my other posts here. But I proceeded with my analysis and I have arrived at some results for which I need your help in the analysis. I sorted the dexseq...
Forum: RNA Sequencing 05-03-2012, 01:56 AM
Replies: 10
Views: 4,190
Posted By r_sitaram
It looks like the image is not rendering. Here is...

It looks like the image is not rendering. Here is it.
Forum: RNA Sequencing 05-03-2012, 01:52 AM
Replies: 10
Views: 4,190
Posted By r_sitaram
Hello Simon, Thanks for that. I...

Hello Simon,
Thanks for that. I downloaded the new vignette and proceeded as stated. Here is the plot between mean count value and...
Forum: RNA Sequencing 05-03-2012, 01:29 AM
Replies: 10
Views: 4,190
Posted By r_sitaram
Hello Craig, I checked my...

Hello Craig,
I checked my dataset with the commands that you mentioned. Everything looks fine. The counts were also read. I just did one change. I got information that my data had 3...
Forum: RNA Sequencing 04-29-2012, 08:00 PM
Replies: 10
Views: 4,190
Posted By r_sitaram
Thank you Craig. I will look into it immediately...

Thank you Craig. I will look into it immediately and get back here.
Forum: RNA Sequencing 04-29-2012, 10:06 AM
Replies: 10
Views: 4,190
Posted By r_sitaram
DEXSeq output not convincing

Hello,
I'm running DEXSeq for finding out the differential exon usage between 3 Wild type and 3 transgenic rat data. I obtained the exon count using the scripts dexseq_count.py and the gff...
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