SEQanswers

Go Back   SEQanswers > Search Forums


Showing results 1 to 25 of 53
Search took 0.00 seconds.
Search: Posts Made By: kbradnam
Forum: Bioinformatics 06-11-2015, 08:27 AM
Replies: 19
Views: 138,958
Posted By kbradnam
I believe the precedent for this is in the 2001...

I believe the precedent for this is in the 2001 publication of the human genome paper (in Nature): http://www.nature.com/nature/journal/v409/n6822/full/409860a0.html

"We used a statistic called...
Forum: Bioinformatics 06-06-2015, 10:07 AM
Replies: 1
Views: 911
Posted By kbradnam
CEGMA does not care about the number of sequences...

CEGMA does not care about the number of sequences in your input assembly. CEGMA was designed to work against genome, not transcriptome, assemblies; so you could have just one (very long) sequence in...
Forum: Bioinformatics 04-24-2015, 07:08 AM
Replies: 1
Views: 1,122
Posted By kbradnam
Sounds like your Unix PATH variable isn't being...

Sounds like your Unix PATH variable isn't being set correctly. Your system can't find genome_mapÖthis is not a CEGMA error per se.

Where did you install the CEGMA binaries and what do you seen...
Forum: Bioinformatics 02-13-2015, 12:40 PM
Replies: 0
Views: 1,043
Posted By kbradnam
Warning: CEGMA is broken under NCBI BLAST+ v2.2.30

The latest version of BLAST+ breaks the CEGMA (http://korflab.ucdavis.edu/Datasets/cegma/) program because it no longer supports a word size of 5 in TBLASTN. This may or may not be a bug: I can't...
Forum: De novo discovery 02-11-2015, 04:10 PM
Replies: 12
Views: 6,817
Posted By kbradnam
Can you run CEGMA with the supplied sample data...

Can you run CEGMA with the supplied sample data to check whether the problem is with your CEGMA installation or with your sequence data file?
Forum: Bioinformatics 01-26-2015, 09:20 AM
Replies: 12
Views: 5,445
Posted By kbradnam
As time marches along, there will only ever be...

As time marches along, there will only ever be more problems like this because CEGMA has been locked in development using some older versions of tools. As people install newer versions of things like...
Forum: Bioinformatics 10-09-2014, 07:15 AM
Replies: 4
Views: 1,759
Posted By kbradnam
CEGMA sort of assumes that your genome assembly...

CEGMA sort of assumes that your genome assembly will be complete enough to have at least one core gene. When that doesn't happen you will see strange error messages. The clue in your output is:
...
Forum: Bioinformatics 09-23-2014, 08:19 AM
Replies: 9
Views: 2,631
Posted By kbradnam
Hmm. That is odd. This is part of CEGMA that I...

Hmm. That is odd. This is part of CEGMA that I don't fully understand myself (I didn't write the code) and this is not something I can easily check I'm afraid. We have no current funding to support...
Forum: Bioinformatics 09-22-2014, 02:07 PM
Replies: 9
Views: 2,631
Posted By kbradnam
I don't see this: $ cut -f 1 -d " "...

I don't see this:

$ cut -f 1 -d " " completeness_cutoff.tbl > 248_CEG_ids.txt
$ grep ">" kogs.fa | sed 's/.*___//' | sort -u > 458_CEG_ids.txt
$ grep -f 248_CEGs_ids.txt 458_CEG_ids.txt | wc...
Forum: Bioinformatics 09-22-2014, 08:21 AM
Replies: 9
Views: 2,631
Posted By kbradnam
I've expanded in some more details on your...

I've expanded in some more details on your questions in a blog post, which includes more information about functional annotations of KOGs in particular:
...
Forum: Bioinformatics 09-22-2014, 07:19 AM
Replies: 9
Views: 2,631
Posted By kbradnam
Basically, all output from CEGMA apart from the...

Basically, all output from CEGMA apart from the output.completeness_report file is referring to the larger set of 458 CEGs. The last file generated by CEGMA is output.completeness_report and that is...
Forum: Bioinformatics 09-18-2014, 01:50 PM
Replies: 9
Views: 2,631
Posted By kbradnam
Hi, The kogs.fa file contains 6 proteins per...

Hi,

The kogs.fa file contains 6 proteins per KOG. One for each species used to generate the subset of 458 KOGs. The main part of CEGMA is to determine which of these 458 core eukaryotic genes...
Forum: Bioinformatics 09-12-2014, 03:27 PM
Replies: 7
Views: 3,206
Posted By kbradnam
Remember, these are not scores per se. 'Complete'...

Remember, these are not scores per se. 'Complete' and 'partial' refer to the number of full-length, or full-length *and* partial length core genes detected by the CEGMA pipeline.

Our ideal...
Forum: Bioinformatics 09-11-2014, 08:32 AM
Replies: 7
Views: 3,206
Posted By kbradnam
202 is better than 201 but not as good as 203....

202 is better than 201 but not as good as 203. It's all relative. CEGMA is most useful in this regard only if you have made multiple assemblies from the same input data. This allows you to assess the...
Forum: Bioinformatics 09-08-2014, 07:59 AM
Replies: 1
Views: 1,157
Posted By kbradnam
Alternatives to installing CEGMA yourself

There are many recent threads in which people have reported problems in trying to install and/or run CEGMA. I try to check on these and add comments as time allows, but I thought it worth mentioning...
Forum: Bioinformatics 09-08-2014, 07:53 AM
Replies: 7
Views: 3,206
Posted By kbradnam
Genewise is usually the problem step in most...

Genewise is usually the problem step in most errant runs of CEGMA. As well as the Amazon instance that peromhc mentioned there are many other ways of running CEGMA where you don't have to install it...
Forum: Bioinformatics 09-08-2014, 07:45 AM
Replies: 3
Views: 1,773
Posted By kbradnam
From the location where you ran CEGMA, is there a...

From the location where you ran CEGMA, is there a valid path to ./data/hmm_profiles?
Forum: Bioinformatics 09-08-2014, 07:43 AM
Replies: 1
Views: 1,384
Posted By kbradnam
Did you run CEGMA on your own data, or with the...

Did you run CEGMA on your own data, or with the supplied sample data? Try the sample data first.
Forum: Bioinformatics 09-08-2014, 07:43 AM
Replies: 12
Views: 5,445
Posted By kbradnam
Does the output before this stage imply that you...

Does the output before this stage imply that you have no core genes? I.e. sometimes when you run CEGMA, the initial BLAST step might only find a small number of core genes. Each successive filtering...
Forum: Bioinformatics 05-16-2014, 07:56 AM
Replies: 6
Views: 5,560
Posted By kbradnam
I blogged about this very topic yesterday: ...

I blogged about this very topic yesterday:

http://www.acgt.me/blog/2014/5/15/fun-with-an-error-message-from-ncbi-blast

It is not a great 'error' message'. Actually, it's a warning message that...
Forum: Bioinformatics 05-13-2014, 10:09 AM
Replies: 6
Views: 1,675
Posted By kbradnam
Just a quick update that I've published an...

Just a quick update that I've published an analysis of this survey (which had over 370 responses).

The Extent of Gender Bias in Bioinformatics...
Forum: Bioinformatics 05-06-2014, 02:13 PM
Replies: 6
Views: 1,675
Posted By kbradnam
Hi swbarnes2, It gets very tricky to do...

Hi swbarnes2,

It gets very tricky to do things like you suggest. Historically, there was a clearer division between bioinformaticians who came from biological backgrounds, and those who came from...
Forum: Bioinformatics 05-06-2014, 07:51 AM
Replies: 6
Views: 1,675
Posted By kbradnam
Hi mgogol, I completely agree that a short,...

Hi mgogol,

I completely agree that a short, informal survey like this will not provide answers about the pervasiveness of subtle biases. I deliberately wanted to keep the survey very short and...
Forum: Bioinformatics 05-05-2014, 09:14 PM
Replies: 12
Views: 2,222
Posted By kbradnam
Hmm, I'm not sure if that is one of the...

Hmm, I'm not sure if that is one of the command-line options supported by CEGMA. You'd have to dig around the code to see where that is configured, and I'm afraid I can't help you with that.
Forum: Bioinformatics 05-05-2014, 08:31 AM
Replies: 6
Views: 1,675
Posted By kbradnam
What is the extent of gender bias in bioinformatics? Please help me find out.

Hi,

Iím curious about the extent of gender bias in bioinformatics, so if you consider yourself as someone who does bioinformatics at any level (including studying for a degree/PhD), please...
Showing results 1 to 25 of 53

 


All times are GMT -8. The time now is 10:20 PM.


Powered by vBulletin® Version 3.8.9
Copyright ©2000 - 2020, vBulletin Solutions, Inc.
Single Sign On provided by vBSSO