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Search: Posts Made By: AntonioRFranco
Forum: Bioinformatics 12-03-2015, 12:18 PM
Replies: 7
Views: 3,983
Posted By AntonioRFranco
Take a look to the Masurca assembler ...

Take a look to the Masurca assembler
http://www.ncbi.nlm.nih.gov/pubmed/23990416
Forum: Literature Watch 11-13-2015, 08:20 AM
Replies: 2
Views: 5,152
Posted By AntonioRFranco
A new experience published with Oxford Nanopore

http://jac.oxfordjournals.org/content/70/10/2775.full.pdf+html
Forum: Bioinformatics 08-31-2015, 07:21 AM
Replies: 4
Views: 1,110
Posted By AntonioRFranco
It is time to use a R package such as edgeR,...

It is time to use a R package such as edgeR, DESeq2, etc
It will do the differential expression analysis for you
Forum: Bioinformatics 08-24-2015, 10:56 PM
Replies: 1
Views: 1,904
Posted By AntonioRFranco
You don't mention what OS are you using, but at...

You don't mention what OS are you using, but at least in Windows, you require administrative rights to be able to install or even update packages
Forum: Bioinformatics 07-06-2015, 02:08 AM
Replies: 4
Views: 1,522
Posted By AntonioRFranco
I don't know how well it works, but I heard about...

I don't know how well it works, but I heard about a kmer optimizer that can be used for Velvet. It is named kmergenie (http://kmergenie.bx.psu.edu/)
Forum: Bioinformatics 06-12-2015, 01:19 AM
Replies: 4
Views: 3,108
Posted By AntonioRFranco
You must decide what value use to trim your...

You must decide what value use to trim your sequences for quality
A filter of Q33 is pretty high. If you use that value, you will discard many useful sequences

Where is the border?

SOme users...
Forum: Bioinformatics 06-12-2015, 01:10 AM
Replies: 4
Views: 3,108
Posted By AntonioRFranco
Q33 is a measure of sequencing quality. You can...

Q33 is a measure of sequencing quality. You can get more information from THIS LINK (http://en.wikipedia.org/wiki/FASTQ_format)

You must get rid off of sequences that are badly sequenced because...
Forum: Bioinformatics 06-08-2015, 02:03 AM
Replies: 2
Views: 2,095
Posted By AntonioRFranco
Thank you. It works..

Thank you. It works..
Forum: Bioinformatics 06-07-2015, 11:22 PM
Replies: 2
Views: 2,095
Posted By AntonioRFranco
Problems compiling MCScanX

This is a nice program to look for synteny.
You download the program, do a simple make, and theoretically, you get the executable bin

But I am facing problems, maybe because I have a 64bit Ubuntu...
Forum: Bioinformatics 05-18-2015, 07:02 AM
Replies: 5
Views: 1,480
Posted By AntonioRFranco
Exactly. You only mentioned the directory where...

Exactly. You only mentioned the directory where your db are kept. You need to point out the name of that db
Forum: Bioinformatics 04-25-2015, 01:25 AM
Replies: 4
Views: 1,491
Posted By AntonioRFranco
Take a look to Blast2Go The pro version will...

Take a look to Blast2Go
The pro version will speed your searching by using their Cloud faciltites, and you can use your own local databases as well
Forum: Bioinformatics 04-24-2015, 06:47 AM
Replies: 1
Views: 1,098
Posted By AntonioRFranco
It you access the help, you can read it can be...

It you access the help, you can read it can be attributed to many causes. Contamination of your samples can be one, but not the only
Forum: Bioinformatics 04-22-2015, 02:28 AM
Replies: 1
Views: 1,170
Posted By AntonioRFranco
There is a chance that both versions of the...

There is a chance that both versions of the program are using a different database. The pro version use to have a more updated version

Pro version has some advantages that are indicated in their...
Forum: Bioinformatics 04-19-2015, 08:21 AM
Replies: 4
Views: 1,633
Posted By AntonioRFranco
Take a look to this page VISTA Tool....

Take a look to this page VISTA Tool. (http://genome.lbl.gov/vista/index.shtml) I sucessfully have recently compared two full steptococcus genomes. I eventually process the information that this...
Forum: Bioinformatics 04-19-2015, 08:16 AM
Replies: 3
Views: 1,612
Posted By AntonioRFranco
The inclusion of "X" into a MSF file is the...

The inclusion of "X" into a MSF file is the consequence of having applied a filter for low complexity sequences present into your protein

You can make the choice of turning on or off such as...
Forum: Ion Torrent 02-13-2015, 02:21 AM
Replies: 121
Views: 109,099
Posted By AntonioRFranco
Any update o new thoughts about this thread ?

Any update o new thoughts about this thread ?
Forum: RNA Sequencing 12-18-2014, 12:09 PM
Replies: 48
Views: 9,703
Posted By AntonioRFranco
You can do a whole genome comparison with some...

You can do a whole genome comparison with some programs such as Mauve or Act. There are tutorials around explaining how to use them
Forum: General 12-18-2014, 12:07 PM
Replies: 20
Views: 4,424
Posted By AntonioRFranco
www.cartagenia.com You don't mention if it...

www.cartagenia.com
You don't mention if it should be of free access or not
Forum: SOLiD 09-17-2014, 11:05 PM
Replies: 5
Views: 8,577
Posted By AntonioRFranco
BFast facilitates the fast and accurate mapping...

BFast facilitates the fast and accurate mapping of short reads to reference sequences, where mapping billions of short reads with variants is of utmost importance

You asked control quality. I...
Forum: SOLiD 09-17-2014, 11:42 AM
Replies: 5
Views: 8,577
Posted By AntonioRFranco
I did some quality control in some old SOLiD...

I did some quality control in some old SOLiD reads that a colleague of mine had kept for several years

1. First I merged cfasta and qual SOLiD files in a single fastqc file using solid2fastq.c...
Forum: Introductions 02-18-2013, 03:26 AM
Replies: 0
Views: 821
Posted By AntonioRFranco
Hello from Spain

My name is Antonio and I work in the University of Córdoba in Spain. I entered here for a double purpose: to learn and to get information to teach my students. I am responsible for teaching System...
Showing results 1 to 21 of 21

 


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