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Search: Posts Made By: lcollado
Forum: General 04-06-2011, 09:14 AM
Replies: 30
Views: 11,935
Posted By lcollado
No problem and I'm glad you were able to solve...

No problem and I'm glad you were able to solve your question :)

Leo
Forum: General 04-04-2011, 08:14 AM
Replies: 30
Views: 11,935
Posted By lcollado
Hello srividya, I don't know the answer, but...

Hello srividya,

I don't know the answer, but you can find out using the ASCII table: http://es.wikipedia.org/wiki/ASCII

Solexa fastq (>= 1.3) won't have any values below 64. Meaning that...
Forum: De novo discovery 03-09-2011, 06:26 AM
Replies: 26
Views: 25,410
Posted By lcollado
You could also try using the Columbus module from...

You could also try using the Columbus module from Velvet.
Forum: Introductions 02-10-2011, 09:36 AM
Replies: 2
Views: 724
Posted By lcollado
Hello again, Check the paper on the Panda...

Hello again,

Check the paper on the Panda genome http://dx.doi.org/10.1038/nature08696 . It doesn't answer your question completely, but it's a start.



Greetings,
Leo
Forum: Introductions 02-10-2011, 09:30 AM
Replies: 2
Views: 724
Posted By lcollado
Hello ppbto, You should ask your question in...

Hello ppbto,

You should ask your question in the bioinformatics forum instead of the Introductions one. Anyhow, as I understand it your question is:

Is it possible to estimate the genome size...
Forum: Bioinformatics 02-10-2011, 07:49 AM
Replies: 278
Views: 91,675
Posted By lcollado
Hello, I just began reading this whole...

Hello,

I just began reading this whole thread (and skipped some of the longer posts :P) and I would like to know what is the current status with CS data. In some of the older posts you mention a...
Forum: De novo discovery 02-10-2011, 07:36 AM
Replies: 4
Views: 3,600
Posted By lcollado
You can always aling your reads against your...

You can always aling your reads against your contigs and determine any inconsistencies. The group at the Broad Institute proposed in their ALLPATHS papers other ways to evaluate assemblies.

Leo
Forum: De novo discovery 02-10-2011, 07:34 AM
Replies: 26
Views: 25,410
Posted By lcollado
While I would like to agree with you because I...

While I would like to agree with you because I would be able to use this tool in our de novo assembly projects, I understand that part of their success is based on the different kinds of input data....
Forum: De novo discovery 02-08-2011, 09:00 AM
Replies: 26
Views: 25,410
Posted By lcollado
This claim got my attention as we've had good...

This claim got my attention as we've had good results using the current VelvetOptimiser.

By the way, there is a new version available of ALLPATHS: its ALLPATHS-LG (Larger Genomes). It requires...
Forum: Literature Watch 12-01-2010, 01:49 PM
Replies: 12
Views: 4,275
Posted By lcollado
I haven't been able to download it from it's main...

I haven't been able to download it from it's main site: http://henrystewart.metapress.com/app/home/contribution.asp?referrer=parent&backto=issue,5,7;journal,1,23;linkingpublicationresults,1:121141,1...
Forum: Bioinformatics 11-30-2010, 07:23 AM
Replies: 1
Views: 1,459
Posted By lcollado
Check this thread on how to install AMOS: ...

Check this thread on how to install AMOS:
http://seqanswers.com/forums/showthread.php?t=3712&highlight=amos
Forum: Literature Watch 11-30-2010, 07:19 AM
Replies: 12
Views: 4,275
Posted By lcollado
Haha ok :) Anyhow, I did end up download several...

Haha ok :) Anyhow, I did end up download several of the papers :)
Forum: Literature Watch 11-29-2010, 03:20 PM
Replies: 12
Views: 4,275
Posted By lcollado
no kidding! so many posts for 1 day :eek:

no kidding! so many posts for 1 day :eek:
Forum: De novo discovery 11-15-2010, 11:30 PM
Replies: 7
Views: 3,477
Posted By lcollado
Hello Blaize, I just checked (a few times)...

Hello Blaize,

I just checked (a few times) the recent mails from the list and I cannot find yours. So it most likely didn't get sent to the mailing list and I recommend you to re-send it.
...
Forum: De novo discovery 11-15-2010, 12:25 AM
Replies: 7
Views: 3,477
Posted By lcollado
Hello Blaize, You should probably ask this...

Hello Blaize,

You should probably ask this question on the Velvet mailing list where Daniel Zerbino will most likely answer it:
http://listserver.ebi.ac.uk/mailman/listinfo/velvet-users
...
Forum: Bioinformatics 10-25-2010, 10:38 AM
Replies: 27
Views: 10,187
Posted By lcollado
Hello, I just installed AMOS on a computer...

Hello,

I just installed AMOS on a computer after not doing so for months. I just wanted to point out that instead of doing it the way Eskeww proposed, it's quite easy to do it as lechu502 posted. ...
Forum: Bioinformatics 09-02-2010, 08:31 AM
Replies: 1
Views: 10,470
Posted By lcollado
Hello, The next 2 threads have a lot of...

Hello,

The next 2 threads have a lot of information on RNA-seq and calculating expression levels (RPKM, ...).

Smile how to study differential expression?...
Forum: Service Providers 09-02-2010, 08:23 AM
Replies: 162
Views: 119,111
Posted By lcollado
Just posting a minor update. The name changed a...

Just posting a minor update. The name changed a little bit from UUSM to:

Unidad Universitaria de Secuenciación Masiva de DNA (http://uusmd.unam.mx/)
Forum: Illumina/Solexa 08-26-2010, 08:17 PM
Replies: 2
Views: 1,451
Posted By lcollado
I have seen the same thing! I hadn't thought...

I have seen the same thing!

I hadn't thought of your 1st point and it makes complete sense :) Just so others understand it, say that at cycle 1 you have a cluster at tile: 1, X: 2, Y: 3. However,...
Forum: Illumina/Solexa 08-26-2010, 08:17 AM
Replies: 2
Views: 1,451
Posted By lcollado
Why do some Ns have higher quality values than other Ns?

Hello,

I was recently discussing Illumina FASTQ files with someone and the following question came up:
Why do some Ns have higher quality values than other Ns? Shouldn't they all be the same?
...
Forum: General 03-03-2010, 08:59 AM
Replies: 8
Views: 2,398
Posted By lcollado
:o nice :) Mexico has more visitors than what I...

:o nice :) Mexico has more visitors than what I would have guessed.
Forum: De novo discovery 03-01-2010, 08:42 PM
Replies: 58
Views: 35,233
Posted By lcollado
I was checking the huge sea of blogs and posts on...

I was checking the huge sea of blogs and posts on ABGT 2010 and found this one to be related: http://www.fejes.ca/2010/02/agbt-2010-brian-haas-broad.html

@jjohnson
Velvet can run with SOLiD data...
Forum: Literature Watch 03-01-2010, 11:02 AM
Replies: 1
Views: 1,113
Posted By lcollado
Nature Methods: A genome in time

A genome in time
Irene Kaganman

Abstract

Addition of next-generation sequencing to an assay of replication timing enables high-resolution genome-scale analyses of multiple cell types.
...
Forum: Illumina/Solexa 03-01-2010, 09:32 AM
Replies: 8
Views: 3,265
Posted By lcollado
Thanks for your feedback ^_^ And well, the...

Thanks for your feedback ^_^

And well, the bottom up for me starts at base calling because I'm not into chemistry. I do get your point though :)
Forum: Bioinformatics 03-01-2010, 09:30 AM
Replies: 7
Views: 2,107
Posted By lcollado
Thank you for your feedback :)

Thank you for your feedback :)
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