Forum: Illumina/Solexa
04-24-2009, 05:47 PM
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Replies: 9
Views: 7,118
I can't really advise on #2, but I strongly...
I can't really advise on #2, but I strongly suggest that you cut relatively high and narrow. If you have a good control over your insert size, the paired-endedness will be more informative.
Ali
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Forum: RNA Sequencing
04-24-2009, 05:32 PM
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Replies: 49
Views: 37,152
Hi Melissa,
Let me see if I can answer your...
Hi Melissa,
Let me see if I can answer your questions.
The reference to "pooled tissues" is that the RNA-samples (coming from a third party) were not from a single mouse brain but from many...
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Forum: RNA Sequencing
04-24-2009, 12:36 PM
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Replies: 25
Views: 14,039
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Forum: RNA Sequencing
04-24-2009, 09:36 AM
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Replies: 25
Views: 14,039
Hi,
So I would take the error message to...
Hi,
So I would take the error message to heart that malloc (the unix memory allocation call) is failing - which implies that you are running out memory. Could you (or someone else) be using up...
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Forum: RNA Sequencing
04-24-2009, 09:12 AM
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Replies: 49
Views: 37,152
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Forum: Illumina/Solexa
04-16-2009, 02:38 PM
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Replies: 9
Views: 10,896
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Forum: RNA Sequencing
04-16-2009, 02:36 PM
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Replies: 25
Views: 14,039
Hi Vix,
Honestly, compared to the RNA-seq...
Hi Vix,
Honestly, compared to the RNA-seq pipeline, the ChIP-seq pipeline is pretty fast (but maybe I'm not objective about this!)
The basis of the original algorithm is still as described in...
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Forum: RNA Sequencing
04-16-2009, 02:26 PM
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Replies: 10
Views: 20,211
Hi Warren,
ERANGE currently assumes a fixed...
Hi Warren,
ERANGE currently assumes a fixed read length & isn't particularly mixed read-length friendly. It's a topic that's been on my mind a lot lately and I plan on fixing it.
Some of these...
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Forum: Illumina/Solexa
04-14-2009, 08:35 AM
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Replies: 9
Views: 10,896
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Forum: RNA Sequencing
04-14-2009, 08:28 AM
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Replies: 10
Views: 20,211
ERANGE for non-Illumina data
Hi Warren,
I'm sorry if I didn't get back to you by email!
I certainly don't have any explicit support for SOLiD colorspace; since we only have Illumina sequencers at Caltech, I don't even have...
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Forum: RNA Sequencing
04-14-2009, 08:18 AM
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Replies: 25
Views: 14,039
ERANGE performance, etc...
I can see how my rather sparse documentation could lead people astray.
Performance-wise, you need to make sure that you have 3 things under control:
1) You need to allocate as much cache as...
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Forum: RNA Sequencing
02-23-2009, 12:57 PM
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Replies: 25
Views: 14,039
Re: Also struggling with ERANGE...
Hi,
The error message is about not finding cistematic (cistematic.caltech.edu), which is a required package to use ERANGE for RNA-seq !
If you've already downloaded cistematic (and the...
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Forum: Literature Watch
06-22-2008, 05:31 PM
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Replies: 3
Views: 3,734
Which name henceforth ?
Ok, I am genuinely curious to know what people think of the three acronyms and which one will last.... I must say that while I've heard a multitude of people use the term RNA-seq at conferences and...
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Forum: Introductions
06-22-2008, 10:32 AM
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Replies: 1
Views: 2,407
Hello from Pasadena
Hello,
My name is Ali. I've had a couple of publications on ChIP-seq and RNA-seq over the last year, which feels like an eternity. Since I see that people are posting here, I thought I'd join the...
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