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Forum: Bioinformatics 08-03-2011, 05:48 AM
Replies: 292
Views: 144,179
Posted By Bruins
Dear all, I'm had the same problem as...

Dear all,

I'm had the same problem as oudacontrol above and Jeckow earlier in this thread.

Trying to get samtools view to extract one chromosome from a sorted and indexed bam file fails:...
Forum: RNA Sequencing 03-30-2011, 12:41 AM
Replies: 2
Views: 1,153
Posted By Bruins
"isoforms n.plu. (1) the different forms of a...

"isoforms n.plu. (1) the different forms of a polymorphic protein; (2) two or more proteins or RNAs that are produced from the same gene by differential transcription and/or differential RNA...
Forum: Bioinformatics 03-30-2011, 12:18 AM
Replies: 15
Views: 2,236
Posted By Bruins
Have you read the mirDeep publication? ...

Have you read the mirDeep publication?

miRDeep (http://www.ncbi.nlm.nih.gov/pubmed/18392026)
Deciphering the porcine intestinal microRNA transcriptome....
Forum: General 03-28-2011, 05:34 AM
Replies: 11
Views: 2,977
Posted By Bruins
Interesting thread! Strangely enough (I work...

Interesting thread!

Strangely enough (I work with exomes every day): no, thank you. It's an uncomfortable thought having my sequenced DNA lying around somewhere.

I should in fact take some time...
Forum: Bioinformatics 03-28-2011, 05:21 AM
Replies: 1
Views: 3,908
Posted By Bruins
Carefully read your stack trace: If the...

Carefully read your stack trace:

If the problem isn't the dir you're writing in, use an alternative temp dir (in stead of the default /tmp) with sufficient space (check Picard manual).
Forum: Bioinformatics 03-23-2011, 01:06 AM
Replies: 3
Views: 2,876
Posted By Bruins
Fedora 10 is no longer maintained (11 and 12 are...

Fedora 10 is no longer maintained (11 and 12 are EOL as well and 13 will follow in May one month after the release of 15). I suggest switching to Fedora 14 as soon as possible (15 will be ready in...
Forum: Genomic Resequencing 03-23-2011, 12:40 AM
Replies: 14
Views: 4,001
Posted By Bruins
Hi, 1. The danger of aligning to only a...

Hi,

1. The danger of aligning to only a certain region is that the aligner will try to find a spot for all reads in that region. This means that reads that do not belong there will be placed...
Forum: Bioinformatics 03-22-2011, 07:59 AM
Replies: 7
Views: 2,686
Posted By Bruins
You can also use the GATK. In case you're...

You can also use the GATK.

In case you're new to the whole thing: I recommend making templates for each of the analysis steps you take, and then run some script to replace the placeholders with...
Forum: Introductions 03-16-2011, 08:48 AM
Replies: 4
Views: 2,945
Posted By Bruins
Yeah, I tend to keep it general as well, for the...

Yeah, I tend to keep it general as well, for the same reason: people losing interest in their own question.

@Joann: that is a pretty cool picture, thanks!

So I work at the hospital's genetics...
Forum: Bioinformatics 03-15-2011, 11:56 PM
Replies: 12
Views: 4,854
Posted By Bruins
Hi John, Did you already choose and install...

Hi John,

Did you already choose and install a distro, or are you first awaiting some answers here? In that case, the choice for a distro is kind of personal. I'm a Fedora person (have been since...
Forum: Bioinformatics 03-03-2011, 04:13 AM
Replies: 11
Views: 3,671
Posted By Bruins
dingxiaofan1, is this what you mean?

dingxiaofan1, is this what you mean?
Forum: Bioinformatics 03-03-2011, 03:46 AM
Replies: 365
Views: 159,919
Posted By Bruins
Hi Simon and others, I have a question...

Hi Simon and others,

I have a question regarding thresholds for the per sequence quality scores.

We did a lot of whole exomes on our Illumina machines and for each sample I generate a QC...
Forum: Bioinformatics 03-03-2011, 02:51 AM
Replies: 11
Views: 3,671
Posted By Bruins
you mean that it's not a default because it is...

you mean that it's not a default because it is always the case? That's what I expected, I gues I just used the word default wrong :P
Forum: Bioinformatics 03-03-2011, 01:49 AM
Replies: 11
Views: 3,671
Posted By Bruins
They are. True. I haven't used samtools...

They are.

True.

I haven't used samtools tview so I don't know what blue or green means.

I'm not entirely sure I understand your question, so pardon me if I'm telling you stuff you already...
Forum: Bioinformatics 03-02-2011, 03:56 AM
Replies: 11
Views: 3,671
Posted By Bruins
just a thought, but are you perhaps confusing...

just a thought, but are you perhaps confusing base call scores, mapping scores and SNP call scores, all 3 of which are represented as Phred scores?
Forum: Bioinformatics 02-22-2011, 11:25 PM
Replies: 48
Views: 56,463
Posted By Bruins
Thanks for all the above posts, very helpful!

Thanks for all the above posts, very helpful!
Forum: Bioinformatics 02-22-2011, 11:21 PM
Replies: 1
Views: 3,309
Posted By Bruins
just a hunch: you are a regular user. Try being...

just a hunch: you are a regular user. Try being root (su -).
Forum: Bioinformatics 02-22-2011, 11:00 PM
Replies: 16
Views: 7,122
Posted By Bruins
I want that! I want that! :D Yeah... one...

I want that! I want that! :D


Yeah... one of us rcently had a kid so shooting wasn't an option. We now resort to yelling and SciFi. :cool:
Forum: Bioinformatics 02-22-2011, 07:31 AM
Replies: 16
Views: 7,122
Posted By Bruins
We see what Westerman said earlier: disk IO...

We see what Westerman said earlier: disk IO trouble. Our solution is access to the university's cluster (http://www.rug.nl/cit/hpcv/publications/docs/millipede), which we share with other research...
Forum: Bioinformatics 02-10-2011, 12:26 AM
Replies: 17
Views: 6,030
Posted By Bruins
Were these data sequenced one sample per lane...

Were these data sequenced one sample per lane (which I expect), or multiple samples per lane?

Were other, non cancer cell line samples sequenced on the same run as cancer cell line samples? (I...
Forum: General 02-09-2011, 11:56 PM
Replies: 3
Views: 1,404
Posted By Bruins
That has helped me A LOT.

That has helped me A LOT.
Forum: Bioinformatics 02-09-2011, 11:54 PM
Replies: 48
Views: 56,463
Posted By Bruins
I struggle(d) with this too. Googled much, found...

I struggle(d) with this too. Googled much, found little answers. Perhaps an idea to add this kind of thing (where to find docs on file formats + additional explanation) to the wiki? It would help to...
Forum: Bioinformatics 02-09-2011, 11:50 PM
Replies: 11
Views: 2,579
Posted By Bruins
They are unassembled supercontigs. They can be...

They are unassembled supercontigs. They can be found in hg19 (at least, in 1kg.37) but not in hg18.

Can someone confirm if I got this right?

Anyway, we do use them to align to, because there...
Forum: Bioinformatics 01-27-2011, 12:10 AM
Replies: 24
Views: 10,020
Posted By Bruins
@figure002: I PBed you to avoid slow chat in this...

@figure002: I PBed you to avoid slow chat in this thread ;)
Forum: General 01-26-2011, 07:55 AM
Replies: 18
Views: 5,491
Posted By Bruins
Also, getting your local UCSC browser seems like...

Also, getting your local UCSC browser seems like a great idea, but you have 32 bits windows. That just might be a problem. Haven't installed UCSC locally myself but if it does work on your local win...
Showing results 1 to 25 of 78

 


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