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Search: Posts Made By: miguelangel
Forum: Bioinformatics 07-04-2014, 12:27 AM
Replies: 5
Views: 3,998
Posted By miguelangel
Thanks a lot I got exactly the same errors,...

Thanks a lot

I got exactly the same errors, so I will try if with these new files are properly formated to run BLAST.
Forum: Bioinformatics 07-03-2014, 08:23 AM
Replies: 5
Views: 3,998
Posted By miguelangel
I have tried to do the same but using...

I have tried to do the same but using 'makeblastdb' and now I get this different error:

Error: (803.7) Blast-def-line-set.E.title
Bad char [0x9] in string at byte 38
uncultured bacterium;...
Forum: Bioinformatics 07-03-2014, 07:16 AM
Replies: 5
Views: 3,998
Posted By miguelangel
How can I format RDP database to be used in a BLAST search?

Hello there and thank you for your welcome!

I have to format RDP 16S bacterial database in fasta format (downladed from here:http://rdp.cme.msu.edu/misc/resources.jsp) to fit in a BLAST search,...
Forum: Bioinformatics 12-13-2012, 03:12 AM
Replies: 5
Views: 1,236
Posted By miguelangel
I work with fungal ITS sequences, but I have a...

I work with fungal ITS sequences, but I have a lot of reads (+/- 450pb long) of the same region, ITS-1, not correlative short sequences.
Forum: Bioinformatics 12-13-2012, 12:31 AM
Replies: 2
Views: 1,283
Posted By miguelangel
Thanks a lot. I'll try what you say and read...

Thanks a lot.

I'll try what you say and read that page inmediatly and I'll write back then.
Forum: Bioinformatics 12-13-2012, 12:29 AM
Replies: 5
Views: 1,236
Posted By miguelangel
Maybe it is a problem of words: What I want...

Maybe it is a problem of words:

What I want to do is the following:

Seq1: AAAAAAGGGGGCCCCC
Seq2: AAAAAACCCCCTTTTT

---> After processing:

Seq1: A A A A A G G G G G C C C C C - - - - -
Forum: Bioinformatics 12-12-2012, 09:42 AM
Replies: 2
Views: 1,283
Posted By miguelangel
Basic problem while using BWA

I have other recent post asking for the convenience of using BWA-SW for some kind of database.

While I am waiting for your great help, I tried to get into the algorithm. But I have not be able.
...
Forum: Bioinformatics 12-12-2012, 08:50 AM
Replies: 5
Views: 1,236
Posted By miguelangel
Starting to use BWA-SW

I would need to align sequences without any reference database (I have a database, but it is not aligned yet). My idea was to find some software that allows me to align this .fasta file and use it as...
Forum: Bioinformatics 12-03-2012, 02:06 AM
Replies: 4
Views: 2,392
Posted By miguelangel
Thanks a lot. I am going to look about...

Thanks a lot.

I am going to look about gsMapper right now.
Forum: Bioinformatics 12-03-2012, 01:10 AM
Replies: 4
Views: 2,392
Posted By miguelangel
Thanks maubp, but if I am not wrong, BLAT is...

Thanks maubp, but if I am not wrong, BLAT is useful if you work with short/shotgun sequences. It would be also useful for 454 sequences?

I am trying to get started with it, anyway.

Thanks again.
Forum: Bioinformatics 11-30-2012, 04:20 AM
Replies: 4
Views: 2,392
Posted By miguelangel
Align very big .fasta files

Hi!

I need to align big fasta files in any way. I have tried to align them in some web-servers, but my files are too big to be run in there.

I have also tried to align them with some freeware,...
Forum: Metagenomics 09-02-2012, 11:22 PM
Replies: 6
Views: 2,247
Posted By miguelangel
Encantado de poder ayudarte. Mis muestras no...

Encantado de poder ayudarte.

Mis muestras no son de Machu Pichu, pero... ¿por qué lo preguntas? ;)
Forum: Metagenomics 08-31-2012, 03:30 AM
Replies: 6
Views: 2,247
Posted By miguelangel
Muchas gracias por la info! Nosotros estamos...

Muchas gracias por la info!

Nosotros estamos realizando los análisis de secuencias de bacterias, hongos y algas, obtenidas desde un 454 Titanium de Roche.

Por ahora las secuencias parece que...
Forum: Metagenomics 08-31-2012, 01:07 AM
Replies: 6
Views: 2,247
Posted By miguelangel
hello! I'm having similar problems, how do...

hello!

I'm having similar problems, how do you finally resolve them?

By the way, what about the assembly for fungi?

I'm from Madrid, so if you want we can speak in Spanish
Forum: 454 Pyrosequencing 06-04-2012, 11:48 PM
Replies: 2
Views: 1,724
Posted By miguelangel
Thanks a lot. I am doing a metagenomics...

Thanks a lot.

I am doing a metagenomics study.

I think I can start with my trimming, because most of the bases have a quality better than q10, so I only have to erase short ones.

I will try...
Forum: 454 Pyrosequencing 06-04-2012, 08:46 AM
Replies: 2
Views: 1,724
Posted By miguelangel
hello and first questions!

Hello there!

I'm starting with my brand new data from Roche's 454 pyrosequencing and I have some questions at this point.

First of all, I am not very confident with my .qual files. I have...
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