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Forum: Bioinformatics 01-09-2014, 05:56 AM
Replies: 13
Views: 15,462
Posted By Zigster
I received a request for permission to use my...

I received a request for permission to use my awesome diagram from someone but they have Private Messages blocked so I could not respond directly.

In any case, yes feel free to use my awesome...
Forum: Bioinformatics 09-23-2013, 09:47 AM
Replies: 26
Views: 15,897
Posted By Zigster
One thing that I've learned from all commercial...

One thing that I've learned from all commercial bioinformatics software (not just CLC - they are probably the best of the bunch):



At some point a scientist is just going to have to learn how...
Forum: Bioinformatics 09-16-2013, 10:12 AM
Replies: 1
Views: 2,617
Posted By Zigster
Yeah, I tried Aaron's recipe once and got very...

Yeah, I tried Aaron's recipe once and got very low numbers (although siblings were higher than strangers). I think the no-calls is screwing it up.
Forum: Bioinformatics 01-15-2013, 11:45 AM
Replies: 37
Views: 8,039
Posted By Zigster
You are either a troll or unfamiliar with how...

You are either a troll or unfamiliar with how scientific software is developed. I will assume the latter.

Scientific software is written largely by the underpaid masses in academia. Many of these...
Forum: Bioinformatics 04-12-2012, 01:38 PM
Replies: 13
Views: 15,462
Posted By Zigster
well i think you accumulate badness from the 3'...

well i think you accumulate badness from the 3' end, though I suppose you wind up with the same result in your approach

> cumsum(-(rev(QS)-THR))
[1] 7 12 9 7 7 7 14 14 14 11 8 ...
Forum: Bioinformatics 04-03-2012, 07:24 AM
Replies: 2
Views: 10,204
Posted By Zigster
you can go from GFF to GRanges without stopping...

you can go from GFF to GRanges without stopping at GTF

gffRangedData<-import.gff("myFile.gff)
myGranges<-as(gffRangedData, "GRanges")
Forum: Bioinformatics 01-10-2012, 12:17 PM
Replies: 3
Views: 3,460
Posted By Zigster
Yes that's true. If someone says RNA-Seq they are...

Yes that's true. If someone says RNA-Seq they are implying something reference-based is being done on the dry side. Someone would have to say de novo transcriptome assembly for me to think otherwise,...
Forum: Bioinformatics 11-06-2011, 03:00 PM
Replies: 21
Views: 10,689
Posted By Zigster
I don't know whether to laugh or cry ...

I don't know whether to laugh or cry

http://www.google.com/search?q=bioconductor+ngs
Forum: Bioinformatics 11-03-2011, 04:51 AM
Replies: 13
Views: 15,462
Posted By Zigster
here is an awesome diagram I have devoted hours...

here is an awesome diagram I have devoted hours to:

accumulate badness right to left
trim at max badness
...
Forum: Bioinformatics 08-23-2011, 05:34 AM
Replies: 5
Views: 4,890
Posted By Zigster
no, looks like you have found a metric that works...

no, looks like you have found a metric that works for you. N50 is not the last word in assemblies.


This approach is fairly innocuous (it just clusters sequences with 100% one-sided overlap), you...
Forum: Bioinformatics 08-05-2011, 08:27 AM
Replies: 19
Views: 140,089
Posted By Zigster
the N50 (L50) should actually be a value in the...

the N50 (L50) should actually be a value in the list of contigs lengths- the Broad "mathematical definition" is faulty since the median is not even a set member
Forum: Bioinformatics 03-15-2011, 12:29 PM
Replies: 3
Views: 2,126
Posted By Zigster
yes you have made the correct observation, they...

yes you have made the correct observation, they are basically one in the same except in the latter you walk away a new reference from your consensus
Forum: Bioinformatics 03-08-2011, 06:48 AM
Replies: 31
Views: 9,982
Posted By Zigster
Is this presentation available?

Is this presentation available?
Forum: Bioinformatics 02-22-2011, 05:58 AM
Replies: 43
Views: 27,098
Posted By Zigster
(Hi Simon, emailed you but that might have been...

(Hi Simon, emailed you but that might have been blocked with attachments)

I notice DESeq is calling low or zero fold change genes as significantly differentially expressed in situations with no...
Forum: Bioinformatics 01-29-2011, 08:01 PM
Replies: 43
Views: 27,098
Posted By Zigster
From the DESeq paper: ...

From the DESeq paper:




SampleA SampleB
Gene1 10000 20000
Gene2 15000 25000
Forum: Bioinformatics 01-28-2011, 05:44 AM
Replies: 31
Views: 9,982
Posted By Zigster
yes please post it

yes please post it
Forum: Bioinformatics 01-06-2011, 07:45 AM
Replies: 31
Views: 9,982
Posted By Zigster
I don't know where you got the word "HashMap"...

I don't know where you got the word "HashMap" from - I think that is Java. Any association between reads and their kmers is for the purposes of paired-end resolution and read usage statistics.

Are...
Forum: Bioinformatics 01-05-2011, 11:12 AM
Replies: 9
Views: 5,752
Posted By Zigster
i don't think you loaded ShortRead start R ...

i don't think you loaded ShortRead
start R

in R:
Forum: De novo discovery 12-28-2010, 09:03 AM
Replies: 1
Views: 4,659
Posted By Zigster
http://www.google.com/search?q=Optimal+k-mer+and+N...

http://www.google.com/search?q=Optimal+k-mer+and+N50

there are a ton of links here.

please do some research and come back with a precise question.
Forum: Bioinformatics 12-27-2010, 12:06 PM
Replies: 31
Views: 9,982
Posted By Zigster
The diagram on the top is the actual order (known...

The diagram on the top is the actual order (known only to the organism being sequenced)

The graph below it would represent what an assembler could piece from short reads.
Four contigs would be...
Forum: Bioinformatics 12-27-2010, 11:39 AM
Replies: 31
Views: 9,982
Posted By Zigster
the repeat problem is the primary reason for...

the repeat problem is the primary reason for fragmented assemblies

http://seqanswers.com/forums/attachment.php?attachmentid=612&stc=1&d=1293482060

the ambiguities here cannot be resolved so the...
Forum: Bioinformatics 12-27-2010, 10:30 AM
Replies: 31
Views: 9,982
Posted By Zigster
Reads are not the actors in a Velvet assembly,...

Reads are not the actors in a Velvet assembly, only kmers, so any mention of k-1 always refers to kmers (two kmers get an edge if they overlap by k-1).

So forget about reads, at least until the...
Forum: Bioinformatics 12-14-2010, 06:57 AM
Replies: 2
Views: 1,620
Posted By Zigster
right now "./s_1_sorted.bam" is just a character...

right now "./s_1_sorted.bam" is just a character vector, a string

load your BAM file into something compatible with the 'subject' of countOverlaps: a Ranges, RangesList, or RangedData. So check...
Forum: Bioinformatics 12-08-2010, 05:24 PM
Replies: 5
Views: 2,664
Posted By Zigster
that comes from an old version of Bioconductor ...

that comes from an old version of Bioconductor

Install R 2.12.0 then reinstall Bioconductor
Forum: Bioinformatics 12-08-2010, 01:45 PM
Replies: 292
Views: 159,195
Posted By Zigster
What is the safest way to reheader a BAM file...

What is the safest way to reheader a BAM file generated by an alignment to the human_g1k_v37.fasta genome, i.e.


to something that would be more compatible with the UCSC-centric Bioconductor...
Showing results 1 to 25 of 116

 


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