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Forum: Bioinformatics 11-15-2009, 08:05 PM
Replies: 236
Views: 587,057
Posted By apfejes
Depends what you're trying to do - I've used...

Depends what you're trying to do - I've used Vancouver Short Read Analysis Package/FindPeaks (my own software) for RNA-Seq (alternative exon expression) and had good luck - I don't use it in windows,...
Forum: Bioinformatics 10-27-2009, 08:11 AM
Replies: 236
Views: 587,057
Posted By apfejes
We use a database of all predicted/potential...

We use a database of all predicted/potential exon/exon junctions in addition to the genome, and then use maq/bwa - it seems to do very well.
Forum: Bioinformatics 10-17-2009, 01:57 PM
Replies: 236
Views: 587,057
Posted By apfejes
Hi Elia, The short answer is that you don't...

Hi Elia,

The short answer is that you don't need to run separateReads/SortReads on map files, as the reads they contain are already sorted by chromosome and start position. Of course, if you're...
Forum: Bioinformatics 10-09-2009, 12:18 PM
Replies: 236
Views: 587,057
Posted By apfejes
Hi Ka123$, I emailed it to you last week. ...

Hi Ka123$,

I emailed it to you last week. If it didn't arrive, it may be that it was too large. Can you check on the maximum email attachment size your email can accept? The attachment was...
Forum: Bioinformatics 09-30-2009, 08:15 PM
Replies: 236
Views: 587,057
Posted By apfejes
Hi Ka123$, I'm sorry - I can't seem to find...

Hi Ka123$,

I'm sorry - I can't seem to find your email address. Could you send it to me again? I'll package up a copy for you in the morning.

Anthony
Forum: Bioinformatics 09-30-2009, 04:40 PM
Replies: 236
Views: 587,057
Posted By apfejes
Hi Ka123$, Thanks for the detailed report! ...

Hi Ka123$,

Thanks for the detailed report! I've managed to re-create the problem by parsing a data set that is similar. I observed that the iterator crashes on reads marked with "QC", so I've...
Forum: Bioinformatics 09-30-2009, 03:11 PM
Replies: 236
Views: 587,057
Posted By apfejes
Hi Ka123$, Once again, it would really help...

Hi Ka123$,

Once again, it would really help if you tell us what the error is that you're seeing. The most common errors are:

- Trying to write to a directory without permissions
- missing a...
Forum: Bioinformatics 09-28-2009, 02:16 PM
Replies: 236
Views: 587,057
Posted By apfejes
Hi kmcarr - thanks for the clarification. I...

Hi kmcarr - thanks for the clarification. I was under the impression that Gerald was simply one step in the process, rather than a wrapper around the Eland calls. It's getting harder and harder...
Forum: Bioinformatics 09-28-2009, 11:46 AM
Replies: 236
Views: 587,057
Posted By apfejes
Hi ka123$, kmcarr is right - Gerald is an...

Hi ka123$,

kmcarr is right - Gerald is an intermediate program along the way from the sequencing machine to getting results. It's not an appropriate place to look for files to work with...
Forum: Bioinformatics 09-28-2009, 08:52 AM
Replies: 236
Views: 587,057
Posted By apfejes
Hi Ka123$, Gerald and bustard are files...

Hi Ka123$,

Gerald and bustard are files produced by the Illumina Pipeline, as far as I know, and neither one should contain useful information about the origin of a fragment. Only output from an...
Forum: Bioinformatics 09-24-2009, 10:22 AM
Replies: 236
Views: 587,057
Posted By apfejes
I seem to recall that bowtie is able to produce...

I seem to recall that bowtie is able to produce .map files - which would be pre-sorted and directly readable by FindPeaks without breaking it up into chromosomes. That might be a good first pass to...
Forum: Bioinformatics 09-24-2009, 09:43 AM
Replies: 236
Views: 587,057
Posted By apfejes
Hi Ka123, There are other ways to do the...

Hi Ka123,

There are other ways to do the sort - including several methods you could try from the linux command line. However, I'm really not sure why it's taking so memory. Could you give me a...
Forum: Bioinformatics 08-20-2009, 07:19 AM
Replies: 236
Views: 587,057
Posted By apfejes
Hi Dinny, I think there is also a way to get...

Hi Dinny,

I think there is also a way to get Bowtie to produce it's own alignment in .map format, if I recall correctly.

Anyhow, if you're working with SET, you can also convert the bowtie...
Forum: Bioinformatics 08-19-2009, 08:58 AM
Replies: 236
Views: 587,057
Posted By apfejes
Hi Dinny, Findpeaks can use bowtie's reads -...

Hi Dinny,

Findpeaks can use bowtie's reads - but it depends if you want to use PET or SET tags. if you're using PET, you'll need to convert your reads into BED format, which is the only way that...
Forum: Bioinformatics 08-18-2009, 03:27 PM
Replies: 236
Views: 587,057
Posted By apfejes
Hey, that's awesome - Great Job!

Hey, that's awesome - Great Job!
Forum: Bioinformatics 08-05-2009, 09:14 AM
Replies: 236
Views: 587,057
Posted By apfejes
Hi hrajasim, That's a very open ended...

Hi hrajasim,

That's a very open ended question, depending very strongly on what type of analysis you'd like to do. As far as I'm aware, the cutting edge development for NGS is happening in open...
Forum: Bioinformatics 06-15-2009, 07:24 AM
Replies: 236
Views: 587,057
Posted By apfejes
Sorry for the double post - I'm obviously not...

Sorry for the double post - I'm obviously not awake enough this morning. This seems like the perfect application for a Google Knol. (A panel of experts maintaining a single page, wiki stye.)
...
Forum: Bioinformatics 06-15-2009, 07:18 AM
Replies: 236
Views: 587,057
Posted By apfejes
I can check if my hosting will allow one to be...

I can check if my hosting will allow one to be installed - for the moment, I'm not even close to using up my bandwidth. Albeit, the domain name doesn't have much to do with next gen sequencing, but...
Forum: Bioinformatics 06-07-2009, 07:51 PM
Replies: 236
Views: 587,057
Posted By apfejes
Thanks ECO, It's so hard to stay one step...

Thanks ECO,

It's so hard to stay one step ahead of the spammers. I probably should have refreshed before replying. Sorry to those who are getting excessive emails. :/

Anthony
Forum: Bioinformatics 06-07-2009, 07:37 PM
Replies: 236
Views: 587,057
Posted By apfejes
spam? The hidden link is pretty sneaky.

spam? The hidden link is pretty sneaky.
Forum: Bioinformatics 05-14-2009, 12:00 PM
Replies: 236
Views: 587,057
Posted By apfejes
I have a fairly complete set of RNA-Seq tools in...

I have a fairly complete set of RNA-Seq tools in the Vancouver Short Read Analysis Package, although they've never been published.
Forum: Bioinformatics 08-11-2008, 09:28 AM
Replies: 236
Views: 587,057
Posted By apfejes
Hi spirit. I didn't know that my blog was...

Hi spirit.

I didn't know that my blog was THAT famous.... certainly I didn't think I had that many people reading it. I'm glad to know it's been useful to you, however. (=

As for the...
Forum: Bioinformatics 08-09-2008, 04:08 PM
Replies: 236
Views: 587,057
Posted By apfejes
Hi Kmay, I don't see anything at that link...

Hi Kmay,

I don't see anything at that link about the Zoom aligner, which is what I was asking for benchmarks against.

Did I miss something?

Anthony
Forum: Bioinformatics 08-08-2008, 04:08 PM
Replies: 236
Views: 587,057
Posted By apfejes
(ECO, if you're reading this, spirit's reply...

(ECO, if you're reading this, spirit's reply might be deserving of it's own thread.)

Hi Spirit,

First of all, thanks for the long and complete answer. It sounds like a fantastic program -...
Forum: Bioinformatics 08-08-2008, 01:51 PM
Replies: 236
Views: 587,057
Posted By apfejes
I suppose the PET comes out in the format...

I suppose the PET comes out in the format provided by whichever base caller you use. I imagine it wouldn't be too difficult to convert to the formats ZOOM requires.

I believe that people here are...
Showing results 1 to 25 of 35

 


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