Forum: Bioinformatics
05-13-2014, 06:30 AM
|
Replies: 2
Views: 2,425
|
Forum: Bioinformatics
03-24-2014, 06:11 AM
|
Replies: 5
Views: 2,297
|
Forum: General
02-28-2014, 05:20 PM
|
Replies: 10
Views: 2,491
|
Forum: Metagenomics
02-20-2014, 09:06 PM
|
Replies: 6
Views: 4,077
|
Forum: Sample Prep / Library Generation
02-20-2014, 09:01 PM
|
Replies: 8
Views: 2,192
|
Forum: Events / Conferences
02-10-2014, 06:42 AM
|
Replies: 4
Views: 1,713
|
Forum: Pacific Biosciences
02-05-2014, 04:58 AM
|
Replies: 7
Views: 3,840
|
Forum: Bioinformatics
12-14-2013, 11:32 AM
|
Replies: 2
Views: 2,176
|
Forum: Bioinformatics
11-22-2013, 07:09 AM
|
Replies: 5
Views: 1,956
BLAST 1.x!!!
I assume you are trying to...
BLAST 1.x!!!
I assume you are trying to align a lot of sequences; otherwise it is probably about a page of code in any modern programming language & a good exercise for a beginning student.
|
Forum: Pacific Biosciences
11-20-2013, 06:19 AM
|
Replies: 9
Views: 4,325
|
Forum: Pacific Biosciences
11-19-2013, 12:46 PM
|
Replies: 9
Views: 4,325
Hybrid in sense that assembly is driven by two...
Hybrid in sense that assembly is driven by two technologies.
There are all sorts of variants of hybrids -- cleaning reads (as you've described), co-assembly, merging independent assemblies made...
|
Forum: Bioinformatics
11-05-2013, 06:36 AM
|
Replies: 2
Views: 1,445
|
Forum: General
10-22-2013, 08:38 PM
|
Replies: 4
Views: 4,214
|
Forum: Pacific Biosciences
10-22-2013, 08:54 AM
|
Replies: 7
Views: 4,776
The program reads the all_norm.fa file which...
The program reads the all_norm.fa file which contains all the reads without length filtering (at least if you are using HBAR_WF.py) -- it defaults to that name but otherwise takes an argument.
...
|
Forum: Bioinformatics
10-22-2013, 08:31 AM
|
Replies: 10
Views: 2,627
Sounds like a dare! It's really a trivial...
Sounds like a dare! It's really a trivial program & good template for writing other programs that transform sequence data. A good exercise is to use Getopt::Long to set the cutoff size and overlap...
|
Forum: Bioinformatics
10-18-2013, 06:48 PM
|
Replies: 24
Views: 10,095
|
Forum: Pacific Biosciences
10-16-2013, 10:10 AM
|
Replies: 7
Views: 4,776
I'm not sure how to get this within the SMRT...
I'm not sure how to get this within the SMRT Portal environment, but there is a utility called length_Info.py which can be applied to your reads to get an idea of a good length cutoff. This is...
|
Forum: 454 Pyrosequencing
10-01-2013, 10:23 AM
|
Replies: 6
Views: 4,422
Knowing the genome size within an order of...
Knowing the genome size within an order of magnitude is essential. Also, why use 454? You will pay a much higher price per read than with other technologies. Perhaps for a long amplicon it will be...
|
Forum: Introductions
10-01-2013, 07:09 AM
|
Replies: 5
Views: 2,355
|
Forum: Ion Torrent
09-27-2013, 05:56 AM
|
Replies: 122
Views: 111,478
|
Forum: Metagenomics
09-27-2013, 05:53 AM
|
Replies: 1
Views: 1,805
|
Forum: MGISEQ (FKA Complete Genomics)
09-18-2013, 06:02 AM
|
Replies: 9
Views: 13,618
|
Forum: MGISEQ (FKA Complete Genomics)
09-17-2013, 06:02 AM
|
Replies: 9
Views: 13,618
There are a number of programs which have been...
There are a number of programs which have been published which assess assemblies given the read data; trying them out is on my to-do list so I can't make a specific recommendation
ALE: Assembly...
|
Forum: The Pipeline
09-13-2013, 06:06 AM
|
Replies: 2
Views: 10,768
|
Forum: Bioinformatics
09-13-2013, 06:04 AM
|
Replies: 5
Views: 4,175
|