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Search took 0.03 seconds. Search: Posts Made By: dan
Forum: Wiki Discussion 09-15-2021, 01:40 PM
Replies: 1
Views: 11,369
Posted By dan
I spent some time and money trying to get the...

I spent some time and money trying to get the wiki back up and running, but it's currently crippled... I could point you at what we currently have.

Cheers
Forum: Wiki Discussion 07-01-2019, 06:38 AM
Replies: 1
Views: 6,420
Posted By dan
I'm in the process of relaunching the wiki. You...

I'm in the process of relaunching the wiki. You guys will be the first to know!
Forum: Bioinformatics 09-09-2016, 02:05 AM
Replies: 3
Views: 7,071
Posted By dan
I see this when my input Fasta has only Ns

I see this when my input Fasta has only Ns
Forum: Bioinformatics 07-21-2016, 06:18 AM
Replies: 4
Views: 2,879
Posted By dan
I'm trying lastz-1.03.73 from here:...

I'm trying lastz-1.03.73 from here: http://www.bx.psu.edu/~rsharris/lastz/newer/

But I don't see lastz_32... Is this now the default behaviour?

I just tried 'make lastz_32' and it appeared :-D...
Forum: Introductions 07-19-2016, 07:29 AM
Replies: 6
Views: 2,954
Posted By dan
Which? ...

Which?
http://www.yandell-lab.org/software/index.html
Forum: Bioinformatics 07-19-2016, 12:50 AM
Replies: 4
Views: 4,210
Posted By dan
Here is a different script to do the same: ...

Here is a different script to do the same:
https://github.com/Ensembl/ensembl-variation/blob/master/scripts/misc/gvf2vcf.pl
Forum: Introductions 07-19-2016, 12:45 AM
Replies: 6
Views: 2,954
Posted By dan
Hi, I also have a 'genomic VCF', that /does/...

Hi,

I also have a 'genomic VCF', that /does/ cover all loci in the genome... Is it still impossible?


Thanks,
Forum: Bioinformatics 07-01-2016, 05:37 AM
Replies: 0
Views: 1,671
Posted By dan
How to read an Affymetrix Axiom genotype (array data) file?

Hi,

I'm trying to put together genotype data for wheat samples from this resource:
http://www.cerealsdb.uk.net/cerealgenomics/CerealsDB/axiom_flapjack.php

The two types of file I get look like...
Forum: Wiki Discussion 12-04-2015, 01:33 AM
Replies: 0
Views: 9,786
Posted By dan
Talking Add information and provenance to your favourite tools on the wiki

Hi Yes,

SEQwiki (http://seqanswers.com/wiki/SEQanswers) now collects information about the 'contact email address' associated with each bioinformatics application (e.g. a mailing list for the...
Forum: Wiki Discussion 10-02-2015, 04:21 PM
Replies: 2
Views: 15,800
Posted By dan
Smile Learn about the technology underlying SEQwiki!

All details here:
https://semantic-mediawiki.org/wiki/SMWCon_Fall_2015
Forum: Bioinformatics 07-03-2015, 07:48 AM
Replies: 6
Views: 2,004
Posted By dan
I agree it's useful, but it's not what I want...

I agree it's useful, but it's not what I want here.
Forum: Bioinformatics 07-03-2015, 02:36 AM
Replies: 6
Views: 2,004
Posted By dan
Lightbulb FASTQ alignment metrics (RNA-Seq)?

Hello,

How do people judge the quality of a FASTQ (short read) alignment? In particular I'm interested in evaluating RNA-Seq alignments, typically (but not exclusively) from ILLUMINA instruments....
Forum: Bioinformatics 01-15-2015, 04:03 AM
Replies: 218
Views: 166,125
Posted By dan
Question Star is generating files like this in the...

Star is generating files like this in the directory I'm running it from:

SJ.out.tab
Log.std.out
Log.out
Log.final.out
Log.progress.out


How can I put those files into a specific...
Forum: Bioinformatics 03-21-2014, 09:28 AM
Replies: 14
Views: 20,354
Posted By dan
Thanks for this post, do you accept doge tips?

Thanks for this post, do you accept doge tips?
Forum: Bioinformatics 03-07-2014, 11:32 PM
Replies: 3
Views: 2,126
Posted By dan
Programmatic access to data in the ENA / GenBank...

Programmatic access to data in the ENA / GenBank is essential. Will you archive or just wrap that data?

Will you build bespoke pipelines for typical analysis? If so, how will you reach community...
Forum: Bioinformatics 03-07-2014, 12:34 PM
Replies: 3
Views: 2,126
Posted By dan
I was thinking of starting a discussion list for...

I was thinking of starting a discussion list for Google genomics (Google group). Anyone got any opinions?

Anyone in yet? I'd quite like to try the tools if nothing else.
Forum: Bioinformatics 02-17-2014, 12:47 AM
Replies: 6
Views: 5,368
Posted By dan
Thanks GenoMax, for some reason it's missing in...

Thanks GenoMax, for some reason it's missing in this 'systems' install (bcftools is an exe, not a dir), but I see it when I re-download here:
http://sourceforge.net/projects/samtools/files/

I...
Forum: Bioinformatics 02-16-2014, 01:38 PM
Replies: 6
Views: 5,368
Posted By dan
Seems vcfutils.pl isn't part of samtools /...

Seems vcfutils.pl isn't part of samtools / bcftools 19... (it was present in release 18). Has it been wrapped into some other script or options for bcftools itself?

Cheers,
Forum: Wiki Discussion 10-02-2013, 02:21 AM
Replies: 13
Views: 28,189
Posted By dan
Draft it on the wiki, then anyone can edit! ...

Draft it on the wiki, then anyone can edit!

Good luck :D
Forum: Wiki Discussion 10-01-2013, 02:18 PM
Replies: 13
Views: 28,189
Posted By dan
Excellent suggestions! I agree 100% Lets put...

Excellent suggestions! I agree 100%

Lets put this within the 'help' pages of the wiki. I've been very remiss on that front, as there is practically no user-help whatsoever! I think it's a really...
Forum: Wiki Discussion 09-01-2013, 12:48 PM
Replies: 3
Views: 19,491
Posted By dan
How do I 'like' this post ;-) It's a pretty...

How do I 'like' this post ;-)

It's a pretty awesome collection of tools! Many thanks to all the contributors!
Forum: Wiki Discussion 09-01-2013, 12:46 PM
Replies: 8
Views: 39,013
Posted By dan
Fortunately, I was born with enough experience to...

Fortunately, I was born with enough experience to do this work. For everyone else, there's Google.




Sorry for not replying sooner. I've fixed all the serious errors some months back. There's...
Forum: Wiki Discussion 09-01-2013, 12:42 PM
Replies: 1
Views: 16,962
Posted By dan
Hi AniS, I suspect you've posted in the wrong...

Hi AniS, I suspect you've posted in the wrong forum, but... You could try asking your question in an email to the contact address for DESeq listed here:
http://seqanswers.com/wiki/DESeq
Forum: Wiki Discussion 09-01-2013, 12:39 PM
Replies: 13
Views: 28,189
Posted By dan
OK, I've added the email field and filled it in...

OK, I've added the email field and filled it in for about 5 tools:
http://seqanswers.com/wiki/Property:Email_address

Please feel free to start work on the wiki any time :-)
Forum: Wiki Discussion 08-22-2013, 01:21 PM
Replies: 13
Views: 28,189
Posted By dan
Hey Lorena! One of the EDAM devs created a...

Hey Lorena!

One of the EDAM devs created a putative mapping between terms in SEQwiki and EDAM that i put here:
http://seqanswers.com/w/index.php?title=Ontology:EDAM&action=edit&section=4

You...
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