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Forum: Bioinformatics 11-23-2010, 09:31 AM
Replies: 278
Views: 118,138
Posted By mrawlins
Ray has worked great for our work with Illumina...

Ray has worked great for our work with Illumina and 454 reads, but is giving us some trouble in our tests on SOLiD data. Our test set is from the NCBI SRA (run SRR035444, submission SRA009283),...
Forum: Bioinformatics 11-19-2010, 12:59 PM
Replies: 11
Views: 6,980
Posted By mrawlins
So, I haven't posted much lately on this as it's...

So, I haven't posted much lately on this as it's taken a while to get things up and running.

Trans-ABySS doesn't yet officially support colorspace. I was able to (using an inelegant hack) get it...
Forum: Bioinformatics 11-19-2010, 12:29 PM
Replies: 1
Views: 2,366
Posted By mrawlins
Converting to nucleotide space is generally a bad...

Converting to nucleotide space is generally a bad idea. Converting back will sometimes alleviate this problem, but I don't think that's true in this case.

A single mismatch in colorspace will...
Forum: SOLiD 11-18-2010, 09:07 AM
Replies: 5
Views: 2,332
Posted By mrawlins
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...
Forum: RNA Sequencing 11-16-2010, 04:41 PM
Replies: 15
Views: 23,473
Posted By mrawlins
This will depend on what statistics you use to...

This will depend on what statistics you use to determine statistical significance.

If you are using something like a T-test, you really want as many replicates as possible. You can't do these...
Forum: Sample Prep / Library Generation 11-09-2010, 03:13 PM
Replies: 5
Views: 5,912
Posted By mrawlins
On our bacterial samples we see quite a few SOLiD...

On our bacterial samples we see quite a few SOLiD reads that map to tRNA locations. Even when we put the error tolerance to be quite low and the seed size to be high there are a lot more tRNA reads...
Forum: RNA Sequencing 11-08-2010, 10:54 AM
Replies: 1
Views: 2,209
Posted By mrawlins
Try putting the quals file right between the -Q...

Try putting the quals file right between the -Q and -o switches.
Forum: Bioinformatics 11-04-2010, 08:47 AM
Replies: 4
Views: 4,695
Posted By mrawlins
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...
Forum: RNA Sequencing 11-04-2010, 08:43 AM
Replies: 15
Views: 18,840
Posted By mrawlins
What we've used for time-course models is doing a...

What we've used for time-course models is doing a pair-wise comparison of each time point with the control (time 0) after quantile normalization. We've had a lot of success with doing a Fisher Exact...
Forum: Bioinformatics 11-02-2010, 03:16 PM
Replies: 11
Views: 6,980
Posted By mrawlins
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...
Forum: Sample Prep / Library Generation 11-02-2010, 12:24 PM
Replies: 2
Views: 2,164
Posted By mrawlins
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...
Forum: Bioinformatics 11-02-2010, 12:17 PM
Replies: 25
Views: 8,353
Posted By mrawlins
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...
Forum: Bioinformatics 11-02-2010, 12:00 PM
Replies: 25
Views: 8,353
Posted By mrawlins
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...
Forum: Bioinformatics 11-01-2010, 04:36 PM
Replies: 11
Views: 6,980
Posted By mrawlins
Well, I figured out a little bug I had with ABySS...

Well, I figured out a little bug I had with ABySS and now trans-ABySS is running ( in -1 mode) so we'll see how it turns out. My first impressions are:

This is not production-ready code.

ABySS...
Forum: Bioinformatics 11-01-2010, 09:57 AM
Replies: 14
Views: 10,259
Posted By mrawlins
I would check whether or not your drive is full,...

I would check whether or not your drive is full, write-protected and/or that you have permissions to write to the drive/directory in question. It mostly looks like the drive is full and you'd have...
Forum: SOLiD 10-28-2010, 10:29 AM
Replies: 3
Views: 1,795
Posted By mrawlins
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...
Forum: Bioinformatics 10-27-2010, 12:02 PM
Replies: 11
Views: 6,980
Posted By mrawlins
I did get 1.2.4 running. So far we haven't run...

I did get 1.2.4 running. So far we haven't run any pair-end or mate-pair experiments, so I wouldn't be able to replicate your problem.
It looks like you've got an assert that failed, which is...
Forum: Bioinformatics 10-27-2010, 09:54 AM
Replies: 11
Views: 6,980
Posted By mrawlins
That bash script should work... I was way...

That bash script should work... I was way over-thinking this problem.

Thanks!
Forum: Bioinformatics 10-26-2010, 03:45 PM
Replies: 11
Views: 6,980
Posted By mrawlins
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...
Forum: Bioinformatics 10-25-2010, 09:30 AM
Replies: 5
Views: 12,869
Posted By mrawlins
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...
Forum: General 10-21-2010, 10:40 AM
Replies: 2
Views: 2,542
Posted By mrawlins
Using blast is likely a terrible idea if you have...

Using blast is likely a terrible idea if you have tons of data. It just isn't fast enough. A wide array of software have been designed to do match your Illumina reads to the genome. My personal...
Forum: Bioinformatics 10-19-2010, 11:09 AM
Replies: 11
Views: 3,324
Posted By mrawlins
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...
Forum: SOLiD 10-15-2010, 01:31 PM
Replies: 5
Views: 4,708
Posted By mrawlins
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...
Forum: General 10-14-2010, 02:44 PM
Replies: 3
Views: 2,661
Posted By mrawlins
GA can also be stand for Genetic Algorithm (one...

GA can also be stand for Genetic Algorithm (one approach at data analysis not often used with sequencing data) or Global Arrays (one approach at using multiple processor to analyze data, also not...
Forum: Bioinformatics 10-06-2010, 03:19 PM
Replies: 514
Views: 225,013
Posted By mrawlins
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)...
Showing results 1 to 25 of 63

 


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