Forum: General
05-09-2011, 12:49 PM
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Replies: 1
Views: 1,360
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,...
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Forum: Bioinformatics
11-11-2010, 02:51 PM
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Replies: 3
Views: 1,235
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...
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Forum: Bioinformatics
01-06-2010, 09:46 AM
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Replies: 4
Views: 2,943
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
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Forum: Bioinformatics
01-06-2010, 08:19 AM
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Replies: 4
Views: 2,943
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...
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Forum: Events / Conferences
03-17-2009, 09:23 PM
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Replies: 23
Views: 9,937
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...
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Forum: Events / Conferences
03-17-2009, 03:39 PM
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Replies: 23
Views: 9,937
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Forum: Events / Conferences
03-16-2009, 11:05 AM
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Replies: 23
Views: 9,937
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...
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Forum: Bioinformatics
02-04-2009, 04:21 PM
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Replies: 5
Views: 3,435
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
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Forum: Bioinformatics
10-22-2008, 03:26 PM
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Replies: 3
Views: 2,595
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
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Forum: Bioinformatics
10-11-2008, 08:07 AM
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Replies: 52
Views: 84,431
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...
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Forum: Bioinformatics
10-10-2008, 12:19 PM
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Replies: 24
Views: 20,425
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...
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Forum: Bioinformatics
10-07-2008, 09:57 AM
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Replies: 24
Views: 20,425
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?...
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Forum: Bioinformatics
10-07-2008, 09:46 AM
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Replies: 52
Views: 84,431
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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