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Search: Posts Made By: dan
Forum: Bioinformatics 09-09-2016, 02:05 AM
Replies: 3
Views: 5,345
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: 1,490
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: 1,407
Posted By dan
Which? ...

Which?
http://www.yandell-lab.org/software/index.html
Forum: Bioinformatics 07-19-2016, 12:50 AM
Replies: 4
Views: 2,938
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: 1,407
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: 597
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: 2,532
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: 0
Views: 1,930
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: 872
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: 872
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: 113,929
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: 13,184
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: 1,241
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: 1,241
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: 2,063
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: 2,063
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: 12
Views: 19,839
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: 12
Views: 19,839
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: 11,837
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: 7
Views: 23,488
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: 10,020
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: 12
Views: 19,839
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: 12
Views: 19,839
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...
Forum: Bioinformatics 08-12-2013, 08:25 AM
Replies: 30
Views: 5,237
Posted By dan
Smile Yay! Keep up the good work :D

Yay! Keep up the good work :D
Forum: Bioinformatics 07-30-2013, 01:59 PM
Replies: 30
Views: 5,237
Posted By dan
Huge thanks for working on this Björn! Can you...

Huge thanks for working on this Björn! Can you not just log in to WP to get round the captcha issue? Hmm... I see you have a user account... Do you still get this problem?

I see what you've been...
Showing results 1 to 25 of 265

 


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