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Forum: Bioinformatics 02-13-2012, 12:58 PM
Replies: 3
Views: 2,891
Posted By jts
Try the program fastaFromBed in bedtools: ...

Try the program fastaFromBed in bedtools:

http://code.google.com/p/bedtools/
Forum: Bioinformatics 09-17-2011, 05:25 AM
Replies: 2
Views: 1,759
Posted By jts
You may be interested in this paper, which...

You may be interested in this paper, which describes a similar strategy:

http://genome.cshlp.org/content/21/5/734.short
Forum: Bioinformatics 07-11-2011, 11:20 AM
Replies: 4
Views: 2,420
Posted By jts
I believe you are looking at the template length...

I believe you are looking at the template length field (field 9). The mapping quality is the 5th field and is reported to be 60 for both reads.
Forum: Bioinformatics 03-30-2011, 02:07 AM
Replies: 6
Views: 4,366
Posted By jts
I use SimSeq by John St. John: ...

I use SimSeq by John St. John:

https://github.com/jstjohn/SimSeq
Forum: Bioinformatics 02-21-2011, 12:24 AM
Replies: 16
Views: 8,396
Posted By jts
I don't know the requirements of the base-calling...

I don't know the requirements of the base-calling pipeline but the amount of RAM you have suggested might be excessive for alignment/variant calling applications, particularly on exomes. I would...
Forum: General 02-14-2011, 08:57 AM
Replies: 1
Views: 1,935
Posted By jts
I have found the SimSeq simulator to be quite...

I have found the SimSeq simulator to be quite useful:

https://github.com/jstjohn/SimSeq
Forum: Bioinformatics 01-28-2011, 05:49 AM
Replies: 2
Views: 1,536
Posted By jts
Are you looking for the circos visualization...

Are you looking for the circos visualization tool?

http://mkweb.bcgsc.ca/circos/
Forum: Bioinformatics 01-10-2011, 04:31 AM
Replies: 8
Views: 4,107
Posted By jts
It varies assembler to assembler. Some will...

It varies assembler to assembler. Some will select the most likely number of copies of the repeat based on read pairs spanning the loop and the insert size distribution. Others will just built a...
Forum: Bioinformatics 01-10-2011, 03:54 AM
Replies: 8
Views: 4,107
Posted By jts
Not quite since the graph contains a loop. Label...

Not quite since the graph contains a loop. Label the nodes as follows:

x = TAGTCGAG
y = GAGGCTTTAGA
z = AGAGACAG
w = AGATCCGAGATGAG

Note that node y branches in both directions (to x/w on...
Forum: Bioinformatics 01-10-2011, 02:11 AM
Replies: 8
Views: 4,107
Posted By jts
I'm not completely clear on what you are asking...

I'm not completely clear on what you are asking but I think you want to know how to decide when to merge distinct nodes in the de Bruijn graph into a single node. This is done when two nodes are...
Forum: RNA Sequencing 01-07-2011, 12:29 AM
Replies: 4
Views: 2,776
Posted By jts
You should try posting your questions to the...

You should try posting your questions to the abyss mailing list:

http://groups.google.com/group/abyss-users
Forum: De novo discovery 12-12-2010, 06:26 AM
Replies: 2
Views: 4,163
Posted By jts
It looks like the perl script simply selects the...

It looks like the perl script simply selects the mode of the k-mer frequency histogram: 1 and 17 are the most frequent values in the two histograms you show. The histogram for k=31 looks as expected...
Forum: Bioinformatics 11-26-2010, 04:17 AM
Replies: 3
Views: 3,170
Posted By jts
Have you seen this paper? ...

Have you seen this paper?

http://bioinformatics.oxfordjournals.org/content/26/10/1284.abstract
Forum: Bioinformatics 11-21-2010, 04:10 AM
Replies: 2
Views: 2,020
Posted By jts
The latest samtools can output vcf through the...

The latest samtools can output vcf through the mpileup program. Take a look at the samtools manual under the heading "Call SNPs and short indels for one diploid individual". I believe this the...
Forum: Bioinformatics 09-10-2010, 01:07 AM
Replies: 2
Views: 4,063
Posted By jts
You may wish to try the recently-released...

You may wish to try the recently-released "Columbus" module for velvet. You can find the manual for it on the velvet webpage here:

http://www.ebi.ac.uk/~zerbino/velvet/
Forum: Bioinformatics 03-24-2010, 11:58 AM
Replies: 2
Views: 2,339
Posted By jts
Hi, The abyss README file should have...

Hi,

The abyss README file should have instructions for running the parallel version of the assembler. If you still have questions, I suggest emailing the abyss users mailing list:...
Forum: Bioinformatics 01-20-2010, 04:53 AM
Replies: 1
Views: 2,591
Posted By jts
Velvet and other de Bruijn graph assemblers...

Velvet and other de Bruijn graph assemblers (abyss, Euler-SR) are able to re-use reads. Each instance of the read contributes the same k-mer path to the graph so removing redundant copies does not...
Forum: Genomic Resequencing 10-09-2009, 06:45 AM
Replies: 3
Views: 5,264
Posted By jts
http://bioinformatics.oxfordjournals.org/cgi/conte...

http://bioinformatics.oxfordjournals.org/cgi/content/short/btp579v1

Is this the paper you are looking for?
Forum: Bioinformatics 09-09-2009, 06:28 PM
Replies: 2
Views: 4,889
Posted By jts
Hi lindseyjane, Abyss supports paired reads....

Hi lindseyjane,

Abyss supports paired reads. The README file included with the source includes instructions on how to assemble paired-end data. If you need more help you can post questions to the...
Forum: Bioinformatics 08-14-2009, 01:09 AM
Replies: 27
Views: 11,114
Posted By jts
Hi NSTbioinformatics, If you post the...

Hi NSTbioinformatics,

If you post the details of your problem on the abyss-users mailing list (http://www.bcgsc.ca/mailman/listinfo/abyss-users) Shaun Jackman or I can help you set up abyss for...
Forum: De novo discovery 05-18-2009, 10:26 AM
Replies: 3
Views: 2,936
Posted By jts
Have you considered using abyss? ...

Have you considered using abyss?

http://www.ncbi.nlm.nih.gov/pubmed/19251739
Forum: Bioinformatics 02-25-2009, 01:34 AM
Replies: 9
Views: 3,586
Posted By jts
Hello Jason, Have you tried Abyss? ...

Hello Jason,

Have you tried Abyss?

http://www.bcgsc.ca/platform/bioinfo/software/abyss
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