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Forum: Bioinformatics 02-24-2010, 10:40 AM
Replies: 4
Views: 1,899
Posted By dcjamison
mgalign also has a much better understanding of...

mgalign also has a much better understanding of spliced alignments than BLAST.

http://proline.bic.nus.edu.sg/mgalign/mgalignit.html

I used this to annotate a velvet assembly and was quite...
Forum: Bioinformatics 02-23-2010, 11:16 AM
Replies: 9
Views: 5,360
Posted By dcjamison
I've done PE vs RefSeq also, and my impression...

I've done PE vs RefSeq also, and my impression (not backed by numbers) is that the majority of anomalies are due to positional issues. I did not pursue it, since I was looking for something...
Forum: Bioinformatics 02-22-2010, 04:50 AM
Replies: 43
Views: 20,324
Posted By dcjamison
We looked at it when it first came out, and it...

We looked at it when it first came out, and it would have involved making too many changes in our data workflow for too little benefit -- lots and lots of scripts to change :(

As things are...
Forum: Bioinformatics 02-20-2010, 11:29 AM
Replies: 43
Views: 20,324
Posted By dcjamison
We are interested in alternative splicing and...

We are interested in alternative splicing and reads which bridge exons. Since we align to RefSeq, we use the RefSeqAli file to convert from RefSeq to genomic coordinates. If you've aligned to the...
Forum: Bioinformatics 02-18-2010, 12:46 PM
Replies: 43
Views: 20,324
Posted By dcjamison
We align our mRNA-Seq to RefSeq then convert the...

We align our mRNA-Seq to RefSeq then convert the alignments to bed format, using the UCSC RefSeqAli table as the source for genomic coordinates and splice boundaries. The bed files are saved as...
Forum: Bioinformatics 12-15-2009, 08:43 AM
Replies: 3
Views: 1,589
Posted By dcjamison
I think the major barrier to writing a GUI is the...

I think the major barrier to writing a GUI is the cost/benefit ratio. Java makes it simple to write a GUI, but what does that GUI actually do for you?

For example, think about what a GUI would...
Forum: Bioinformatics 08-31-2009, 06:49 AM
Replies: 5
Views: 2,443
Posted By dcjamison
The only time a N gets put into the sequence is...

The only time a N gets put into the sequence is when the base caller cannot match a cluster in the current tile. Typically this happens at the edge, when clusters "wander" on and off the image. Based...
Forum: Bioinformatics 04-29-2009, 05:08 AM
Replies: 2
Views: 2,126
Posted By dcjamison
As of 1.3.2, Bustard does the qs calibration...

As of 1.3.2, Bustard does the qs calibration according to an internal table. You can do custom calibration from the command line, so if you want uncalibrated scores in the new format you could create...
Forum: Bioinformatics 04-16-2009, 05:16 AM
Replies: 13
Views: 15,578
Posted By dcjamison
Very nice. One minor issue: "Illumina 1.3...

Very nice. One minor issue:

"Illumina 1.3 format encodes a Phred quality score from 0 to 40 using ASCII 64 to 99."

The "99" should be 104, or else the range is only 0 to 35.

Also, as a very...
Forum: Bioinformatics 03-30-2009, 10:52 AM
Replies: 6
Views: 1,995
Posted By dcjamison
An alternative explanation: The pipeline...

An alternative explanation:

The pipeline parallelizes with different granularities for different tasks. For most steps, the granularity is at the tile level, while for the eland and the reporting...
Forum: Bioinformatics 03-18-2009, 10:58 AM
Replies: 3
Views: 2,277
Posted By dcjamison
No, you cannot use phageAlign for paired ends --...

No, you cannot use phageAlign for paired ends -- the pairing scripts run off the eland_multi output and will not accept the phageAlign output. You can however analyze each end separately -- do an...
Forum: Bioinformatics 01-26-2009, 12:29 PM
Replies: 1
Views: 1,338
Posted By dcjamison
Can you give a bit more context about why you...

Can you give a bit more context about why you want to do this? The prb files are keyed to the seq files, and rearranging the line order will invalidate the mapping.
Forum: Bioinformatics 12-31-2008, 10:41 AM
Replies: 1
Views: 1,691
Posted By dcjamison
ALLPATHS compiling issues

Has anyone recently compiled the current version of ALLPATHS? We downloaded the source from the Broad website and have run into a problem with what looks to be a missing file. The MakeDepends script...
Forum: Illumina/Solexa 11-11-2008, 04:25 AM
Replies: 5
Views: 2,428
Posted By dcjamison
Yes, that is correct. eland_extended also...

Yes, that is correct. eland_extended also produces better output -- the *_export.txt file is much easier to use (in my opinion).
Forum: Illumina/Solexa 11-08-2008, 09:39 AM
Replies: 5
Views: 2,428
Posted By dcjamison
The first 32 bases are used for the seed...

The first 32 bases are used for the seed alignment, then the alignment is extended for the bases beyond 32.

For GA Pipeline 0.3 and newer, there is a Gerald analysis mode called eland_extended...
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