I'm just developing a simple desktop application. you could convert your SOLiD 5500 xsq files to csfasta and quality data using your favorite Linux desktop distribution.
Screenshots:
This is the main window, you can browse and select your xsq files clicking XSQ ==> CSFASTA+QUAL button.
Or you can select File menu then select Load SOLiD 5500 XSQ file menu.
Filter and select your XSQ files.
myXSQ ask you if you want to convert your selected XSQ files to csfasta and qual files.
you will need to configure your output directory where to save your csfasta and quality values first.
Select your Output directory.
Preview of your csfasta and quality files
myXSQ shows important information about licensing ,myXSQ is Software Libre but you will need to get an official XSQ Tools version from Applied Biosystems because I can't distribute XSQ Tools.
myXSQ will support more features.
Hi,
I made some fixes to the code (ldd issues, env vars..etc) of the shell script "convertFromXSQ.sh".
convertFromXSQ.sh shell script try to find $XSQ_TOOLS environment variable first, if $XSQ_TOOLS is defined then set rootDir variable.
Ubuntu Linux 11.04 (Natty) (glibc 2.13)
Step 1. Converting XSQ to CSFASTA/QUAL
(clic screenshots)
Step 2. Results
On July 4th I attended the Workshop "Data Visualization for SOLiD Sequencing Users" which was held at the offices of Life Technologies of Mexico.
Workshop Program:
9:00 - 10:00 Introduction to Bioinformatic Analysis (Leonardo Varuzza PhD. Life Technologies)
10:00 - 14:00 Workshop: Data Visualization using BamViewer, Tablet, Artemis, MochiView, MagicViewer (Winter Genomics)
14:00 - 15:00 meal time ( ohh yes, very good 
)
15:00 - 18:00 LifeScope Software (Leonardo Varuzza PhD. Life Technologies)
Winter Genomics started to speak about Galaxy project and we start to work on Galaxy website but Galaxy's website failed and luckily I had set my own version of Galaxy website on my computer and we can continue working in the workshop
in the end I talk a little about several points:
1. I am debugging the BioScope installation in Debian based Linux distributions, my first tests are sucessfull.
2. Efforts are being developed to use IonTorrent Mapping Tools on Galaxy Project.
3. I developed a small script that allows Galaxy set up reference database for Blast/Megablast
This workshop allow us to meet and share information that is useful for everyone.
Thanks Life Technologies Mexico and Brassil for the first Data Visualization WorkShop and of course thanks to Langebio Genomics Team.
Thanks everyone for the Workshop, it was great event !!
If you are using WTA (Transcriptome) pipeline and you are working with genomes that you have downloaded from the ENSEMBL website, you will need to check the genome annotation identifiers matches the reference genome identifiers.
Bioscope has several scripts and one of them allows to format ENSEMBL genome annotations (*.gtf files) to use UCSC-style identifiers
my Arabidopsis genome annotations has some entries like the following examples:
Mt protein_coding exon 273 734 . - . gene_id "ATMG00010"; transcript_id "ATMG00010.1"; exon_number "1"; gene_name "ORF153A" ; transcript_name "ATMG00010.1"; seqedit "false";
Pt tRNA exon 4 76 . - . gene_id "ATCG00010"; transcript_id "ATCG00010.1"; exon_number "1"; gene_name "TRNH"; transcript_name "ATCG00010.1"; seqedit "false";
I added following code (bold text only) in reformat ensembl script:
l46: if ($fields[0] =~ /([1-9][0-9]?|[XY]|MT|Mt|mt|mT|Pt) /) {
l48: $base =~ s/MT/M/;$base =~ s/Mt/M/;$base =~ s/mt/M/;$base =~ s/mT/M/;$base =~ s/Pt/C/;
when we run patched reformat ensembl script we get:
chrM protein_coding exon 273 734 . - . gene_id "ATMG00010"; transcript_id "ATMG00010.1"; exon_number "1"; gene_name "ORF153A" ; transcript_name "ATMG00010.1"; seqedit "false";
chrC tRNA exon 4 76 . - . gene_id "ATCG00010"; transcript_id "ATCG00010.1"; exon_number "1"; gene_name "TRNH"; transcript_name "ATCG00010.1"; seqedit "false";
it works for me !!
Jacob
Cinvestav Langebio
Viva Mexico
It is well known that for analyzing data is necessary to have computing clusters with many hardware resources.
In past months I've been testing transcriptome mapping using a small computing cluster called "Mazorkita" in my work in LANGEBIO. this computing cluster has few resources of RAM ,so in the last point of transcriptome analysis (wt.merge) of the pipeline the process remained in queue and nothing else happened.
After reviewing, I found that the memory request based on the initial configuration of bioscope and the requirement of each pipeline is defined in the following directory:
$ BIOSCOPEROOT/BioScope-1.3.rBS131-55029_20101119113500/etc/plugins/properties
In this directory you will find the file "wt.merge.properties". this file defines properties like memory request, java heap space, number of nodes and other important properties for transcriptome merge process , in my case just edit the following line ,
memory.request = 15GB
and change it to
memory.request = 7GB
you can now save the properties file and then you could run the whole pipeline using less memory but this is just only for testing !!
Viva Mexico
Maybe the fastest solution to validate outside users in BioScope is to use the same Apache Tomcat.
In past days I developed a web page to control users authentication in BioScope, at this time the access control is handled using password and username key, this key value pair are validated by one database engine, there are some options Sqlite, MySql and PostgreSql . should be easy to parse json or xml files.
If you request BioScope web page, you are redirected to login web page then if you login sucessfully you are redirected to main BioScope web page.
Jacob
Cinvestav - Langebio Mexico
Hi, I developed an interactive tutorial that I titled "Discovering BioScope", this is the first tutorial of many, I will be adding more tutorials for each analysis in BioScope.
Basically in this first tutorial you will learn:
- Mapping Fragment Library.
- Check Cluster Jobs via command line.
- Analyze Mapping Output results.
- Tips.
If you want to watch the interactive tutorials, you will need :
- Mozilla Firefox Browser.
- Adobe Flash Plugin.
- Web Site: Interactive Tutorials
Web Site:
http://www.langebio.cinvestav.mx/bioinformatica/jacob/projects/bioscopeit/
If you think that are useful and if you want comment, please add your comment about this tutorial at link labeled as "Comentarios Recientes".
Tutorials are free like Free Software
Jacob
Cinvestav - Langebio Mexico
Last week at the invitation of Applied Biosystems Mexico I attended a bioscope training. The training and the conference took place at the INMEGEN in Mexico City. The training was taught by Leonardo Varuzza (ABI Brazzil) ,my friend, thank you very much Leonardo, very nice to see you once again.
The training was excellent we were basically working on the bioscope command line(Mapping, Small RNA, Ma to Sam and Bam using ini files and plan files..and more stuff), we work editing configuration files and analyzing the results too.
I also thank very much my friend Herbert Garcia (ABI Mexico) for all your help, I appreciate your help, thanks Herbert nice to see you again.
A salute to dr. Claudia Rangel and Rodrigo Garcia (INMEGEN) thanks for letting me take the course in INMEGEN.
Keo nice to meet you too 
Bye
It was a great meeting. I really liked the Sequencing at the Tipping Point meeting in San Diego, CA. I attended almost all conferences and workshop sessions like Ion Torrent, Semiconductor Sequencing, LifeTech news,Biomedical,Cancer, Bioinformatics Workshop about BioScope, Craig Venter conference, Core Lab Workshop and more important conferences.
I really enjoyed the breakfast,lunch and dinner time where I'm drank a beer with good friends that I met such as Derek Blankenship(left) phD from Institute for Health Care from Dallas and Robert Kirkwood (right) from University of Washington and also I met Janine McMurdie(Life Technologies) and we were talking about BioScope software tool.
I'm sorry I almost forgot but I also met a gentleman Alfredo Hidalgo(Inmegen) and other nice people from Mexico.
Robert later told me about bioscope's feedback meeting...
at the bioscope's meeting I talked a little about to improve or update Bioscope's process installation because in my experience when you begin to install Bioscope in your cluster environment maybe you will need people who has knowledge about linux shell commands and java, later when you finished installation you will need test bioscope's performance and finally you will need to learn how to use Bioscope's cli or its web user interface.
I really like Bioscope, I installed Bioscope , it is a good Bioinformatics tool to analyze the SOLiD data.
Congratulations to the Bioscope's team, Bioscope's software architects, head bioinformatics support, senior managers and everyone who are involved and participating in the project.
Last year I developed a small hack in Bioscope's web user interface, I mean I was developing extra help menu and dialog option to display help weblinks (tutorials, guides, manuals and so) using jrf. url: http://www.langebio.cinvestav.mx/bioinformatica/jacob/?p=18
during the flight to Los Angeles CA I was reading a bit more about SOLiD 4 instrument..
some screenshots about meeting..
at dinner time I met Jason Smith (senior bioinformatics) from Life Technologies, Min Li from the Partek Company and Hugh from Geospiza Inc.
The Jody's McIntyre workshop titled "Core Lab Wokshop" was very interesting and important, my opinion is that we need to use social media today as a free resources like facebook or twitter because they are free resources for your bussines and also you can keep all your customers informed about any changes, news and technical support. I mean if you know how to use social media you can increase your bussiness quickly. LifeTech University, SOLiD Center, SOLiD Community and SOLiD Web Site they are very important resources for customers.
That's all
Thanks for the Life Technologies Sequencing at the Tipping Point meeting.
Thanks to dr. Luis Herrera Estrella and Beatriz Jimenez at Langebio-Cinvestav for support me.
Thanks to Applied Biosystems Mexico team (Sandra Balladares, Mario Posadas, Herbert Garcia and more important people) for support me.
Update: In my current work blog I added a PGM Sequencer video that I made with my Iphone 3G mobile, I just recorded a little the Personal Genome Machine Instrument. I am surprised by this new sequencer acquired by LifeTechologies from the IonTorrent company.
my blog url is http://www.langebio.cinvestav.mx/bioinformatica/jacob/
Jacob
