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Search: Posts Made By: spenthil
Forum: Bioinformatics 10-24-2011, 12:12 PM
Replies: 6
Views: 2,272
Posted By spenthil
This paper might also be of interest: Meta-IDBA:...

This paper might also be of interest: Meta-IDBA: a de Novo assembler for metagenomic data. "We introduce the Meta-IDBA algorithm for assembling reads in metagenomic data, which contain multiple...
Forum: Bioinformatics 10-16-2011, 09:50 AM
Replies: 3
Views: 1,409
Posted By spenthil
Try adding: #include 'string.h' To the top of...

Try adding:
#include 'string.h'
To the top of src/common.cpp. If this doesn't work, post the includes section of the problem file.
Forum: De novo discovery 02-16-2011, 03:19 PM
Replies: 3
Views: 2,731
Posted By spenthil
This has been addressed a few times before: ...

This has been addressed a few times before:
http://seqanswers.com/forums/showthread.php?t=2101...
Forum: Bioinformatics 06-25-2010, 07:51 AM
Replies: 10
Views: 4,744
Posted By spenthil
Also, the AWS console now allows access to S3:...

Also, the AWS console now allows access to S3: http://aws.amazon.com/console/#s3

Haven't used it myself, but it looks nice enough.
Forum: Site Announcements 06-01-2010, 09:31 PM
Replies: 8
Views: 12,355
Posted By spenthil
Awesome, thanks!

Awesome, thanks!
Forum: Site Announcements 06-01-2010, 01:37 PM
Replies: 8
Views: 12,355
Posted By spenthil
Is it possible to configure the RSS feed to...

Is it possible to configure the RSS feed to display more than just the first sentence? Specifically:
Forum: Bioinformatics 05-21-2010, 09:14 AM
Replies: 6
Views: 1,967
Posted By spenthil
Torst confirms this:...

Torst confirms this: http://seqanswers.com/forums/showthread.php?t=5085
and this thread: http://seqanswers.com/forums/showthread.php?t=3214...
Forum: Site Announcements 05-19-2010, 09:41 AM
Replies: 33
Views: 20,507
Posted By spenthil
Yup, fortunately it uses OpenID.

Yup, fortunately it uses OpenID.
Forum: Site Announcements 05-19-2010, 09:19 AM
Replies: 33
Views: 20,507
Posted By spenthil
Take a look at http://stackoverflow.com and...

Take a look at http://stackoverflow.com and http://meta.stackoverflow.com/ - you can *definitely* have discussions on this system (admittedly, this isn't obvious). The best part about this format is...
Forum: De novo discovery 05-19-2010, 09:10 AM
Replies: 1
Views: 1,570
Posted By spenthil
Take a look at Velvet, the Rock Band algorithm...

Take a look at Velvet, the Rock Band algorithm uses long reads to resolve ambiguities in the de Bruijn graph....
Forum: Site Feedback/Suggestions 05-17-2010, 09:53 AM
Replies: 22
Views: 5,566
Posted By spenthil
Eco - I have heard your concerns about...

Eco -
I have heard your concerns about StackExchange before. To be honest, I don't have enough independent background knowledge about the system to have an unbiased opinion one way or another - I...
Forum: Site Feedback/Suggestions 05-16-2010, 08:43 PM
Replies: 22
Views: 5,566
Posted By spenthil
Eco, Definitely agree with your conclusion and...

Eco,
Definitely agree with your conclusion and am a big fan of StackExchange like systems. FYI - http://biostar.stackexchange.com/.

Also look at the changes coming up in StackExchange 2.0:...
Forum: Bioinformatics 04-29-2010, 11:38 AM
Replies: 191
Views: 60,924
Posted By spenthil
Could you post the relevant code?

Could you post the relevant code?
Forum: Bioinformatics 04-27-2010, 01:36 PM
Replies: 10
Views: 4,744
Posted By spenthil
FYI - having the data in the AWS Public Data...

FYI - having the data in the AWS Public Data Catalog/S3 would be neat for people analyzing data on AWS EC2 (their cloud computing infrastructure) because transfering data within a region is free and...
Forum: Bioinformatics 04-25-2010, 09:14 AM
Replies: 4
Views: 1,423
Posted By spenthil
http://www.biomedcentral.com/1471-2105/8/474/figur...

http://www.biomedcentral.com/1471-2105/8/474/figure/F6

(from: http://www.biomedcentral.com/1471-2105/8/474)
Forum: Bioinformatics 04-22-2010, 09:31 AM
Replies: 191
Views: 60,924
Posted By spenthil
Perfect! Side note - pip...

Perfect!

Side note - pip (http://pypi.python.org/pypi/pip) is an awesome easy_install replacement that works great with virtualenv. To use it to install: `pip install HTseq`
Forum: General 04-14-2010, 09:08 AM
Replies: 1
Views: 1,314
Posted By spenthil
http://seqanswers.com/forums/showthread.php?t=368

http://seqanswers.com/forums/showthread.php?t=368
Forum: Bioinformatics 04-14-2010, 09:05 AM
Replies: 4
Views: 2,333
Posted By spenthil
I think she is referring to using distributions...

I think she is referring to using distributions for determining read coverage...

Take a look at Figure. 3 in the Euler-USR paper: http://genome.cshlp.org/content/early/2008/12/03/gr.079053.108
Forum: RNA Sequencing 03-25-2010, 09:19 PM
Replies: 2
Views: 3,208
Posted By spenthil
I am no way qualified to answer this question,...

I am no way qualified to answer this question, but can point you to two papers that I have been meaning to read that do cover this:
http://www.nature.com/nmeth/journal/v5/n7/full/nmeth.1226.html...
Forum: Site Feedback/Suggestions 03-25-2010, 10:17 AM
Replies: 22
Views: 5,566
Posted By spenthil
Click on my "google" link above, it does exactly...

Click on my "google" link above, it does exactly that (don't challenge my google'fu) :P. My point is (which I did not make clear at all), I bet a lot of members aren't aware of the "site:" keyword -...
Forum: Site Feedback/Suggestions 03-25-2010, 10:11 AM
Replies: 22
Views: 5,566
Posted By spenthil
Some things I have found to work in other...

Some things I have found to work in other communities to various degrees of success:
1. A *short* set of instructions on message board etiquette.
2. A way of marking question oriented posts as...
Forum: Site Feedback/Suggestions 03-23-2010, 01:36 PM
Replies: 3
Views: 2,427
Posted By spenthil
Have you tried using the RSS feeds...

Have you tried using the RSS feeds (http://seqanswers.com/forums/showthread.php?t=56)?

I personally use google reader which has a nice mobile interface. There are also native iphone apps which...
Forum: Bioinformatics 03-22-2010, 03:43 PM
Replies: 7
Views: 1,814
Posted By spenthil
CLC's whitepaper summaries many of the above...

CLC's whitepaper summaries many of the above points concisely:
https://docs.google.com/viewer?url=http://www.clcbio.com/files/whitepapers/white_paper_on_de_novo_assembly_on_the_CLC_Assembly_Cell.pdf...
Forum: Bioinformatics 03-21-2010, 01:27 PM
Replies: 3
Views: 2,121
Posted By spenthil
You could always just use "-cov_cutoff auto"...

You could always just use "-cov_cutoff auto" (take a look at the manual), but I prefer to avoid magic when possible.

I would make the graph and use it as a starting point, although I recommend...
Forum: Bioinformatics 03-21-2010, 12:38 PM
Replies: 3
Views: 2,121
Posted By spenthil
Take a look at section 5.2 and 5.3 of the velvet...

Take a look at section 5.2 and 5.3 of the velvet manual (https://docs.google.com/viewer?url=http://www.ebi.ac.uk/~zerbino/velvet/Manual.pdf):
5.2 Choice of a coverage cutoff (14)
5.3 Determining the...
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