Bioinformatics

script launch xsqtools

jacobnix@gmail.com — Fri, 04 Nov 2011 19:31:52 GMT

Follow this unofficial tutorial step by step to run xsq-tools on CentOS Linux 6 and OpenSuse Linux

1. If you are using CentOS Linux 6, OpenSuse Linux check which GNU LIBC version you have installed. you can use this command

[jacob@localhost xsq-tools]$ ldd – -version
ldd (GNU libc) 2.12
Copyright (C) 2010 Free Software Foundation, Inc.
This is free software; see the source for copying conditions. There is NO
warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
Written by Roland McGrath and Ulrich Drepper.

to run xsq-tools you will need GNU libc version 2.5+ !!

2. Get Official xsq-tools software package distribution from LifeTech/ABI

3. Open your favorite Linux console command and untar/unzip xsq-tools package.

4. If you want to convert your xsq solid 5500 output files you will need to use the convertFromXSQ.sh shell script.

5. Backup the official convertFromXSQ.sh shell script.

6. Download unofficial convertFromXSQ.sh shell script and save in your official xsq-tools directory,

7. Download script from here

8. Rename script convertFromXSQ.sh1.txt to convertFromXSQ.sh

9. Set execution permission to shell script ( chmod +x convertFromXSQ.sh )

10. Change to xsq-tools directory using linux command line (cd XSQ_Tools)

11. Extras: You can run unofficial convertFromXSQ.sh shell script like this samples

$ remember, cd XSQ-Tools first

(A) $ ./convertFromXSQ.sh -c data/Frag.xsq

(B, from any location)

$ convertFromXSQ.sh -c /home/jacob/XSQ-Tools/data/Frag.xsq -o $HOME

That’s all.

Notes:

[1] If you do not set XSQ_TOOLS environment variable, the unofficial convertFromXSQ.sh set XSQ_TOOLS environment variable automatically.

[2] Follow LifeTech/ABI official readme documentation to install xsq-tools, the unofficial script updates your .bashrc ,bash_profile in user home directories but I disabled exporting PATH environment variable because I need to do some tests, if you want to run unofficial convertFromXSQ.sh from any location you will need to update and export your PATH environment variable manually.

I hope that help you , it works for me !!

myXSQ for XSQ Tools

jacobnix@gmail.com — Mon, 26 Sep 2011 10:37:08 GMT

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.

[Unofficial] XSQ Tools runs on Ubuntu Linux 11.04

jacobnix@gmail.com — Mon, 19 Sep 2011 09:20:14 GMT

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

testing XSQ Tools on CentOS Linux 6

jacobnix@gmail.com — Wed, 14 Sep 2011 07:53:32 GMT

In recent days I was testing XSQ Tools because I needed to convert some xsq files to csfasta and quality values. I was reading the xsq guide but when I try to run convertFromXSQ.sh shell script for first time the script failed.

[jacob@server XSQ_Tools]$ ./convertFromXSQ.sh -c data/Frag.xsq

This build is only supported on CentOS5+ or RHEL 5+ and1
requires glibc 2.5 or later. The current version is
2.12

I'm using CentOS Linux 6 (64bits) and my glibc version is 2.12. I don't understand why convertFromXSQ.sh script shows that I need glibc 2.5 or later.

[jacob@server XSQ_Tools]$ cat /etc/redhat-release
CentOS Linux release 6.0 (Final)

Which is the problem ? I don't know but I assumed that I needed to check script source code, then I made some fixes to the shell script convertFromXSQ.sh.

The convertFromXSQ.sh shell script try to find if $XSQ_TOOLS environment variable is defined first, if $XSQ_TOOLS exists then set rootDir variable..

[jacob@server XSQ_Tools]$ ./convertFromXSQ.sh -c data/Frag.xsq -o .
XSQ Tools for SOLiD 5500 and 5500xl Instrument Series
Copyright 2011 Life Technologies Corporation. All rights reserved.

Testing XSQ Tools Package
Setting rootDir
rootDir=/home/jacob/Downloads/bio/solid5500/xsq-tools/XSQ_Tools
rootDir=/home/jacob/Downloads/bio/solid5500/xsq-tools/XSQ_Tools
OS Detected CentOS Linux release 6.0 (Final)
glibc version found
glibcVersion=2.12
glibcVersionMajor=2
glibcVersionMinor=12
glibcVersionSubversion=0
xsqconvert CPU_TIME: 9.130
xsqconvert WALL_TIME: 10.179

the result path is /home/jacob/Downloads/bio/solid5500/xsq-tools/XSQ_Tools/Libraries/TestLibrary/F3/reads

and finally

[jacob@server reads]$ ls
Frag_TestLibrary_F3.csfasta Frag_TestLibrary_F3.QV.qual rejects

SOLiD3 reagents

martin.gollery@omixon.com — Wed, 13 Jul 2011 19:46:50 GMT

The word is that SOLiD 3 supplies will be discontinued on Oct. 1. This will have a large impact on the mindset of those considering buying a sequencer vs. farming the work out. After all, if you could not buy gas for your car after it was two years old, you might not want to spend the big bucks to get one, would you? Taking a cab or a bus would suddenly look a lot more economically attractive.

Workshop “Sequencing Data Visualization for SOLiD Users” México 2011

jacobnix@gmail.com — Thu, 07 Jul 2011 09:26:06 GMT

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 !!

Upcoming Cloud Courses

martin.gollery@omixon.com — Fri, 01 Jul 2011 15:58:24 GMT

We are in the planning phases for an NGS analysis course to be held at scenic Lake Tahoe. We will use AWS cloud resources to run the analyses, so there will be a fair amount of cloud training as well. I would appreciate any and all feedback about the following points:

Length of time: I was thinking 2 days. Would midweek or weekend be better?

Time of Year: What season works best? Do you prefer skiing, hiking or kayaking after the class is done? (Although this year you can do all on the same day over the 4th of July weekend)!

Venue: Is a pre/post conference course easier to get to?

Thanks,

Marty Gollery

New mapping tools

martin.gollery@omixon.com — Thu, 09 Jun 2011 21:44:31 GMT

The first tests of the Omixon Read Mapper are looking very good compared to BWA. This algorithm is based on nucleic HMMs, and will not be tied exclusively to SOLiD 4. We will begin support for 5500XL, Illumina and many other systems beginning very shortly.

[UnOfficial Simple Update] BioScope Reformat Ensembl Script

jacobnix@gmail.com — Fri, 03 Jun 2011 22:09:35 GMT

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

BioScope Memory Resources

jacobnix@gmail.com — Wed, 01 Jun 2011 16:16:54 GMT

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

Commercial Software for SOLiD

martin.gollery@omixon.com — Fri, 20 May 2011 21:26:03 GMT

I am trying to get my company listed as a commercial software provider for SOLiD systems. See Omixon.com to see the type of solutions that we provide, as an add-in for CLC, standalone server module or on the cloud. I would like to be added to the list at http://www.appliedbiosystems.com/absite/us/en/home/applications-technologies/solid-next-generation-sequencing/ngs-data-analysis-software/software-community.html

Does anyone know how to do this?

Martin Gollery

Simple User Login System for BioScope

jacobnix@gmail.com — Thu, 17 Mar 2011 23:16:23 GMT

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

Discovering BioScope Tutorials

jacobnix@gmail.com — Wed, 16 Mar 2011 09:26:26 GMT

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

SOLiD Bioinformatics and Conference at INMEGEN Mexico D.F.

jacobnix@gmail.com — Sat, 15 Jan 2011 16:23:33 GMT

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

My notes about Life Technologies Sequencing at the Tipping Point meeting at San Diego CA

jacobnix@gmail.com — Mon, 06 Dec 2010 10:49:49 GMT

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