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Search: Posts Made By: apfejes
Forum: Bioinformatics 06-10-2011, 02:02 AM
Replies: 27
Views: 8,620
Posted By apfejes
Thanks ECO.. it was original. (= In any...

Thanks ECO.. it was original. (=

In any case, I'll have a look at this on monday. I don't have time to look at it until I'm back in Canada. If you haven't heard from me by then, please send me a...
Forum: Bioinformatics 06-09-2011, 06:00 AM
Replies: 27
Views: 8,620
Posted By apfejes
That is some serious spam above - and worse,...

That is some serious spam above - and worse, copied from my own blog!

Anyhow, can you paste the first line of the file? There's probably something simple that's going wrong, eg, you haven't...
Forum: Bioinformatics 06-09-2011, 04:30 AM
Replies: 27
Views: 8,620
Posted By apfejes
You need to put the log file in a directory that...

You need to put the log file in a directory that exists and for which you have write permissions. If the directory you've given above does not exits, then it will not be able to create the log file.
Forum: Bioinformatics 06-08-2011, 11:07 PM
Replies: 27
Views: 8,620
Posted By apfejes
Sorry for the slow reply - I'm currently away at...

Sorry for the slow reply - I'm currently away at a conference.

The latest versions can be found as part of the Vancouver Short Read Analysis Package: http://vancouvershortr.sourceforge.net/
...
Forum: Bioinformatics 04-25-2011, 10:56 PM
Replies: 15
Views: 2,970
Posted By apfejes
Thanks Michael. I really appreciate that. (= ...

Thanks Michael. I really appreciate that. (=

I would like to clarify one thing, however. It's not that the two types of documentation can't be discussed simultaneously, but that they shouldn't be...
Forum: Bioinformatics 04-22-2011, 04:19 PM
Replies: 15
Views: 2,970
Posted By apfejes
Michael: I think you're preaching to the choir -...

Michael: I think you're preaching to the choir - but really, there's a huge difference between documentation for developers and documentation for users. Conflating the two - or trying to discuss...
Forum: Bioinformatics 04-22-2011, 02:40 PM
Replies: 15
Views: 2,970
Posted By apfejes
Hi Michael, I agree about your points when...

Hi Michael,

I agree about your points when applied to "user documentation", but this particular thread was about "code documentation" and I'm not sure they're interchangeable.
Forum: Bioinformatics 04-21-2011, 11:24 AM
Replies: 15
Views: 2,970
Posted By apfejes
Open source code with multiple developers does...

Open source code with multiple developers does tend to have better documentation, by necessity.On the flip side, single person projects don't have the time or necessity to documenting everything. ...
Forum: Bioinformatics 04-21-2011, 08:52 AM
Replies: 15
Views: 2,970
Posted By apfejes
I would also add, "my code is well documented"...

I would also add, "my code is well documented" does not fly with PhD committees either.
Forum: Bioinformatics 03-31-2011, 08:09 AM
Replies: 7
Views: 1,819
Posted By apfejes
That's coming directly from your file - the...

That's coming directly from your file - the aligner is using the name of the file as the chromosome. (You can even see it in the snippet you gave at the top of the thread for chr10.fa)

I seem to...
Forum: Bioinformatics 03-31-2011, 07:30 AM
Replies: 7
Views: 1,819
Posted By apfejes
Great, glad it's working! Anthony

Great, glad it's working!

Anthony
Forum: Bioinformatics 03-25-2011, 09:12 AM
Replies: 7
Views: 1,819
Posted By apfejes
It's available from the svn repository. There...

It's available from the svn repository. There are instructions here: http://sourceforge.net/apps/mediawiki/vancouvershortr/index.php?title=VSRAPBuilding

use svn to get a copy of the source, and...
Forum: Bioinformatics 03-25-2011, 07:25 AM
Replies: 7
Views: 1,819
Posted By apfejes
Hi Adam, This may be a little more...

Hi Adam,

This may be a little more technically challenging, but would you be willing to compile and run from source? I suspect that this problem has been solved in the latest version, which has...
Forum: Bioinformatics 02-23-2011, 08:34 AM
Replies: 4
Views: 2,374
Posted By apfejes
Exome reads are usually aligned against the...

Exome reads are usually aligned against the genome because they are captured from DNA, so, for the most part, you will not have exon-exon junctions in your data set. I'm not quite clear what it is...
Forum: Bioinformatics 02-22-2011, 09:06 PM
Replies: 3
Views: 2,550
Posted By apfejes
For what it's worth, I've exported this from our...

For what it's worth, I've exported this from our local ensembl database. the last two digits tell you the reference version, the two digits before that are the ensembl version.

reference version...
Forum: Bioinformatics 02-22-2011, 08:48 PM
Replies: 4
Views: 2,374
Posted By apfejes
I think the question is not necessarily the right...

I think the question is not necessarily the right one. How do you know you've got your exon-junction-spanning reads spanning exons? I believe we usually align all of our transcriptome reads to...
Forum: Bioinformatics 07-14-2010, 12:20 PM
Replies: 57
Views: 33,315
Posted By apfejes
I doubt there are any generic "text file to *"...

I doubt there are any generic "text file to *" converters out there. If the text file had a format such as bed, we might be able to point you in the right direction.

for the moment, your best...
Forum: Bioinformatics 05-20-2010, 08:14 AM
Replies: 57
Views: 33,315
Posted By apfejes
Hi Miltron, Unfortunately, there isn't. ...

Hi Miltron,

Unfortunately, there isn't. This is simply because it was the easiest way to do the sorting required by other applications in my suite, back when the standard alignment formats...
Forum: Epigenetics 03-19-2010, 10:14 AM
Replies: 9
Views: 5,485
Posted By apfejes
Just as a general comment - and it may not answer...

Just as a general comment - and it may not answer your question, 454 is the least used for ChIP-Seq because you don't need the longer reads, and you do need as many fragments as possible (up to the...
Forum: Bioinformatics 02-17-2010, 10:23 AM
Replies: 57
Views: 33,315
Posted By apfejes
Well, I'm not sure what the problem is, then. I...

Well, I'm not sure what the problem is, then. I haven't ever seen that error being given for any other reasons than the ones I've suggested. If you could cut and paste a few lines before the error...
Forum: Bioinformatics 02-17-2010, 09:47 AM
Replies: 57
Views: 33,315
Posted By apfejes
That Error, I am familiar with. It means you've...

That Error, I am familiar with. It means you've either given it an invalid output directory, or do not have permissions to write to that location. You'll either have to check the output directory...
Forum: Bioinformatics 02-17-2010, 09:39 AM
Replies: 57
Views: 33,315
Posted By apfejes
Hi Genbio, Thanks for the information,...

Hi Genbio,

Thanks for the information, however, what I'm actually looking for is the error you're observing. If it's caused by java, it should give information about where in the code the error...
Forum: Bioinformatics 02-17-2010, 09:26 AM
Replies: 57
Views: 33,315
Posted By apfejes
I've never seen that problem before. Could you...

I've never seen that problem before. Could you provide the full output of the error for me, otherwise I don't know where to begin looking to solve this problem. Java normally gives more verbose...
Forum: Bioinformatics 01-08-2010, 11:08 AM
Replies: 2
Views: 1,164
Posted By apfejes
download a copy of dbsnp130 and then just check...

download a copy of dbsnp130 and then just check against that?
Forum: Bioinformatics 01-08-2010, 10:57 AM
Replies: 8
Views: 7,678
Posted By apfejes
Several sequencing centres do (including the one...

Several sequencing centres do (including the one where I'm currently studying). However, you might want to specify which technology you're looking for, as it may make a difference in terms of what...
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