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Forum: General 05-09-2011, 12:49 PM
Replies: 1
Views: 1,202
Posted By vruotti
FTR-Seq amplification free via Illumina

Hi,
I was just wondering if anybody tried this protocol for amplification free RNA-Seq done in the Illumina platform?

http://www.nature.com/nmeth/journal/v7/n2/abs/nmeth.1417.html

Thanks,...
Forum: Bioinformatics 11-11-2010, 02:51 PM
Replies: 3
Views: 1,125
Posted By vruotti
Hi Simon, We see some variation when doing RNA...

Hi Simon,
We see some variation when doing RNA Seq on human. We read your comment. However, if we look don't allocate reads to individual isoforms then I don't understand how this is different from...
Forum: Bioinformatics 01-06-2010, 09:46 AM
Replies: 4
Views: 2,808
Posted By vruotti
Hi Zigster, You might be right. But, we don't...

Hi Zigster,
You might be right. But, we don't see the same pattern when looking at microarray expression in human. The average expression is about the same for short and long transcripts.

Victor
Forum: Bioinformatics 01-06-2010, 08:19 AM
Replies: 4
Views: 2,808
Posted By vruotti
RNA SEQ Bias toward short transcripts (RPKM)

Hi there.
Just wanted to post this to see if anyone else see this interesting pattern. When taking the average expression (RPKMs) of short genes, say 0.5kb to 2.5kb, we see that the average is much...
Forum: Events / Conferences 03-17-2009, 09:23 PM
Replies: 23
Views: 9,164
Posted By vruotti
Conference update.

Interesting Panel discussion today.
A representative from Illumina, Roche, Solid and Helicos were all side by side answering questions from the audience.

The common problem was scalability. All...
Forum: Events / Conferences 03-17-2009, 03:39 PM
Replies: 23
Views: 9,164
Posted By vruotti
If there is enough interest... How about getting...

If there is enough interest... How about getting together tomorrow Wed. There is a question-answer session at 5:40. Maybe after this session?

If this doesn't work perhaps Thursday during lunch?...
Forum: Events / Conferences 03-16-2009, 11:05 AM
Replies: 23
Views: 9,164
Posted By vruotti
Small Group Gathering regarding aligners

Hello,
I will be attending the CHI conf in San Diego and for the ones that are interested in aligners I would like to propose a small group discussion in between talks.
Date and time will be...
Forum: Bioinformatics 02-04-2009, 04:21 PM
Replies: 5
Views: 3,270
Posted By vruotti
MAQ on cluster

A few comments here.
Here is a nice trick posted by Quang.


Hi Victor,
We use "maq fastq2bfq -n 1000000 ..." to split the reads.
....

Q
Forum: Bioinformatics 10-22-2008, 03:26 PM
Replies: 3
Views: 2,345
Posted By vruotti
Quality score graph

Just wondering if anyone have seen the same problem with cycle 30.
Thanks,:confused:
Victor

http://i494.photobucket.com/albums/rr301/ruotti_madison/Picture105.png
Forum: Bioinformatics 10-11-2008, 08:07 AM
Replies: 52
Views: 82,343
Posted By vruotti
normalization

Hi Chema,
Yeah I see what you mean. I guess most of the conditions we ran so far do not have the a huge amount of genes downregulated in comparison with the rest of the genes studied. We are doing...
Forum: Bioinformatics 10-10-2008, 12:19 PM
Replies: 23
Views: 18,675
Posted By vruotti
More on Quality

Hello,
We are looking a little closer at the quality of one of our runs. Interestingly, we see a pattern in most of our runs right at the 30th cycle. The information from the graph below comes from...
Forum: Bioinformatics 10-07-2008, 09:57 AM
Replies: 23
Views: 18,675
Posted By vruotti
Fastq file outside of GERALD

Hi,
Does anyone know an easy way or an existing program to convert all the .prb files from one particular lane into one fastq file? Similar to the s_1_sequence.txt file but with no filters applied?...
Forum: Bioinformatics 10-07-2008, 09:46 AM
Replies: 52
Views: 82,343
Posted By vruotti
RPKM concern?

Hi Chema,

We have used Wold's (RPMK) method and got very good results. Are you saying that if a particular gene has less coverage (coverage=fewer number of mapped reads) this gene will contribute...
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