Forum: Bioinformatics
11-23-2010, 09:31 AM
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Replies: 278
Views: 118,307
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Forum: Bioinformatics
11-19-2010, 12:59 PM
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Replies: 11
Views: 6,987
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Forum: Bioinformatics
11-19-2010, 12:29 PM
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Replies: 1
Views: 2,373
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Forum: SOLiD
11-18-2010, 09:07 AM
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Replies: 5
Views: 2,336
If you disable the auto-export and export them...
If you disable the auto-export and export them manually using scp you can rename the files when you copy them. This doesn't solve the problem of finding which primary.* to use, though in our case...
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Forum: RNA Sequencing
11-16-2010, 04:41 PM
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Replies: 15
Views: 23,499
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Forum: Sample Prep / Library Generation
11-09-2010, 03:13 PM
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Replies: 5
Views: 5,917
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Forum: RNA Sequencing
11-08-2010, 10:54 AM
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Replies: 1
Views: 2,210
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Forum: Bioinformatics
11-04-2010, 08:47 AM
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Replies: 4
Views: 4,700
For comparing samples of Illumina data I would...
For comparing samples of Illumina data I would use a Fisher Exact Test on quantile-normalized read counts to get a probability that two samples are the same. I'm not sure how I would do the same...
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Forum: RNA Sequencing
11-04-2010, 08:43 AM
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Replies: 15
Views: 18,884
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Forum: Bioinformatics
11-02-2010, 03:16 PM
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Replies: 11
Views: 6,987
Well, I finally got all the ABySS output ready...
Well, I finally got all the ABySS output ready for trans-ABySS only to find that it dies because I don't have paired-end data. Does anyone know if there is a way around this, or does trans-ABySS not...
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Forum: Sample Prep / Library Generation
11-02-2010, 12:24 PM
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Replies: 2
Views: 2,172
I haven't heard of anyone spiking in controls,...
I haven't heard of anyone spiking in controls, though perhaps in a few less common pipelines it is used. As far as I know it's not used for RNA-Seq, SNP calling, genome assembly or ChIP-Seq. The...
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Forum: Bioinformatics
11-02-2010, 12:17 PM
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Replies: 25
Views: 8,363
I don't remember seeing any reads shorter than...
I don't remember seeing any reads shorter than the full 50 bp from our SOLiD machine, so I'm a bit surprised that you report seeing them.
For our analysis we figure that the first roughly 27 bp...
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Forum: Bioinformatics
11-02-2010, 12:00 PM
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Replies: 25
Views: 8,363
It's actually fairly intuitive that mapping the...
It's actually fairly intuitive that mapping the shortened reads provides greater number of mappings. The number of reads with adequate quality out to base N goes up as N shrinks and the probability...
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Forum: Bioinformatics
11-01-2010, 04:36 PM
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Replies: 11
Views: 6,987
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Forum: Bioinformatics
11-01-2010, 09:57 AM
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Replies: 14
Views: 10,269
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Forum: SOLiD
10-28-2010, 10:29 AM
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Replies: 3
Views: 1,797
It would still require the same number of...
It would still require the same number of ligation steps, since each ligation would take the same amount of time. It's true that there would be fewer initial primers, resulting in fewer cycles, but...
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Forum: Bioinformatics
10-27-2010, 12:02 PM
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Replies: 11
Views: 6,987
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Forum: Bioinformatics
10-27-2010, 09:54 AM
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Replies: 11
Views: 6,987
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Forum: Bioinformatics
10-26-2010, 03:45 PM
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Replies: 11
Views: 6,987
Getting Trans-ABySS running
We're interested in testing out Trans-ABySS and comparing it with our other methods for RNA-Seq analysis. It seems to have a lot of potential for metatranscriptomics, since we may not always have a...
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Forum: Bioinformatics
10-25-2010, 09:30 AM
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Replies: 5
Views: 12,875
SOLiD Paired-end with Bowtie
This post is really helpful, addressing Illumina mate-pair and paired-end as well as the SOLiD mate-pair. The newest SOLiD machines also have a paired-end, which as near as I can tell is of the...
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Forum: General
10-21-2010, 10:40 AM
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Replies: 2
Views: 2,549
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Forum: Bioinformatics
10-19-2010, 11:09 AM
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Replies: 11
Views: 3,328
Dealing with 20 million reads makes time...
Dealing with 20 million reads makes time complexity of your algorithms (particularly your loop over the reads) of particular importance. I did some post-processing of SAM files using Picard (Java...
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Forum: SOLiD
10-15-2010, 01:31 PM
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Replies: 5
Views: 4,710
Based on my limited understanding of how TopHat...
Based on my limited understanding of how TopHat works, I would be very hesitant to use reads as short as 30bp. It seems to me you would have a pretty good chance of either the front or the back of...
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Forum: General
10-14-2010, 02:44 PM
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Replies: 3
Views: 2,663
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Forum: Bioinformatics
10-06-2010, 03:19 PM
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Replies: 514
Views: 225,237
The command
chmod ugo+rwx bowtie e_coli...
The command
chmod ugo+rwx bowtie e_coli reads/e_coli_1000.fq
will change permissions (chmod)
for the user, group and others (ugo)
to include reading, writing and executing permissions (+rwx)...
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