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Forum: Illumina/Solexa 04-24-2009, 05:47 PM
Replies: 9
Views: 5,165
Posted By alim
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
Forum: RNA Sequencing 04-24-2009, 05:32 PM
Replies: 49
Views: 29,218
Posted By alim
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...
Forum: RNA Sequencing 04-24-2009, 12:36 PM
Replies: 25
Views: 10,947
Posted By alim
4 Gb RAM should be enough for the amount of reads...

4 Gb RAM should be enough for the amount of reads you have.... especially if you have enough virtual memory (could you also be going low on disk space ?)

If it won't work with this much RAM, then...
Forum: RNA Sequencing 04-24-2009, 09:36 AM
Replies: 25
Views: 10,947
Posted By alim
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...
Forum: RNA Sequencing 04-24-2009, 09:12 AM
Replies: 49
Views: 29,218
Posted By alim
fraction of splice-crossing reads is a function of read length

Hi,

It's nice to see a spirited discussion of what the fractions of reads crossing splice junctions should be (and to be quoted in that debate :) ). I'll just restate what is in retrospect...
Forum: Illumina/Solexa 04-16-2009, 02:38 PM
Replies: 9
Views: 9,376
Posted By alim
Good - then take a look at TopHat & see if it...

Good - then take a look at TopHat & see if it does what you need it to do!
Forum: RNA Sequencing 04-16-2009, 02:36 PM
Replies: 25
Views: 10,947
Posted By alim
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...
Forum: RNA Sequencing 04-16-2009, 02:26 PM
Replies: 9
Views: 12,834
Posted By alim
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...
Forum: Illumina/Solexa 04-14-2009, 08:35 AM
Replies: 9
Views: 9,376
Posted By alim
Is there a soybean reference genome available ? ...

Is there a soybean reference genome available ?

If there is, then consider using TopHat or ERANGE (use the later only if you are ambitious enough to build your own Cistematic genome) to get RPKM...
Forum: RNA Sequencing 04-14-2009, 08:28 AM
Replies: 9
Views: 12,834
Posted By alim
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...
Forum: RNA Sequencing 04-14-2009, 08:18 AM
Replies: 25
Views: 10,947
Posted By alim
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...
Forum: RNA Sequencing 02-23-2009, 12:57 PM
Replies: 25
Views: 10,947
Posted By alim
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...
Forum: Literature Watch 06-22-2008, 05:31 PM
Replies: 3
Views: 2,823
Posted By alim
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...
Forum: Introductions 06-22-2008, 10:32 AM
Replies: 1
Views: 1,478
Posted By alim
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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