SEQanswers

Go Back   SEQanswers > Sequencing Technologies/Companies > SOLiD



Similar Threads
Thread Thread Starter Forum Replies Last Post
LifeScope v2.5 paolo.kunder Bioinformatics 1 02-23-2012 01:46 PM
LifeScope Genomic Analysis Solutions Anelda Bioinformatics 1 02-23-2012 01:36 PM
Lifescope -- license manager westerman SOLiD 12 10-31-2011 11:52 PM

Reply
 
Thread Tools
Old 07-14-2011, 08:01 AM   #1
westerman
Rick Westerman
 
Location: Purdue University, Indiana, USA

Join Date: Jun 2008
Posts: 1,104
Default Lifescope -- results compared to Bioscope

After getting the license problems fixed (see my other post) and learning about the new Lifescope CLI and GUI (more on this later), I was finally able to process two recent Bioscope (BS) runs via Lifescope (LS). The results are mixed however this may due to the types of runs -- neither is 'perfect' -- which makes the "truth" a slippery subject.

The first project is an E.coli-based paired-end (50/35 bp) whole-transcriptome project with filtering against an rRNA database. The sample had a lot of rRNA in it with a consequent low mapping rate to the transcriptome.

The second is Honeybee-based 50bp fragment sequencing without filtering.

As far as mapping and the E. coli project, there were about 5% more reads mapped with Lifescope however about 20% fewer 'properly paired' reads and many more singletons. I am not sure why this is so. Perhaps the rRNA filtering?

For mapping and honeybee, the total number mapped reads for Lifescope vs. Bioscope were within 0.1% of each other.

As far as the interesting-to-the-customer results, for E. coli WT the interesting results are the tag counts of the exons. Lifescope consistently had the same or lower counts than Bioscope. Part of this may be due to 20% fewer paired reads and part of this may be due to Lifescope taking mapping qualities into account. In any case the consistency of the numbers was good -- I would have not liked to see wild swings between LS and BS.

For the honeybee project, the most interesting results are SNPs and small InDels. Unfortunately our customer wanted SNPs called at the 'low stringency' cutoff which, in my opinion, causes a lot of false positives. And, of course, the honeybee genome is not 100% done which can cause additional problems. Bioscope came up with ~60,000 SNPS while Lifescope came up with only 30,000. Comparing the two there were about 22,000 of these SNPs in common. So it is hard to say which program is better.


Overall, as I said, the results are mixed. It is hard to say conclusively that Lifescope provides more accurate results than Bioscope. I really need to use projects that utilize model organisms with really clean data sets. Alas, in our line of work, these are few and far apart. I will post more if and when I get back to Lifescope in a non-production-let's-play-with-it moment. At the moment the new Casava (1.8) is calling to me. Then after that our SOLiD 5500 will be on-line and it will be back to production work for me.
westerman is offline   Reply With Quote
Old 08-07-2012, 06:49 AM   #2
rimpi
Junior Member
 
Location: austria

Join Date: Apr 2012
Posts: 2
Default Lifescope Result Error

I am working with next generation sequencing data(solid 5500).
I am using Lifescope for the analysis but having some problems getting the results.
working with human as well as mouse data as I run the data I get an error message:
1) whole transcriptome fragment mapping:28624271 reads at a maximum of 150000000 reads per job will exceed the maximum number of jobs(100).
2) same answer I get if i do small RNA analysis.

can someone suggest me how to come out of this error...
thanks
rimpi is offline   Reply With Quote
Old 08-07-2012, 10:04 AM   #3
westerman
Rick Westerman
 
Location: Purdue University, Indiana, USA

Join Date: Jun 2008
Posts: 1,104
Default

Since, as far as I know, Lifescope is a pay-for and supported-by ABI software then getting hold of ABI's tech support might provide a faster and more accurate answer. There do not seem to be many Lifescope messages on SeqAnswers. Or perhaps I am just not paying attention since I am no longer using Lifescope (nor working with any SOLiD data).
westerman is offline   Reply With Quote
Old 08-20-2012, 06:09 AM   #4
mbblack
Senior Member
 
Location: Research Triangle Park, NC

Join Date: Aug 2009
Posts: 245
Default

Quote:
Originally Posted by rimpi View Post
I am working with next generation sequencing data(solid 5500).
I am using Lifescope for the analysis but having some problems getting the results.
working with human as well as mouse data as I run the data I get an error message:
1) whole transcriptome fragment mapping:28624271 reads at a maximum of 150000000 reads per job will exceed the maximum number of jobs(100).
2) same answer I get if i do small RNA analysis.

can someone suggest me how to come out of this error...
thanks
With the release of ver. 2.5 Lifescope is no longer a for fee application. However, if you are not an ABI SOLiD system client, I don't know how tech support works so you would have to check out their web site to see your options.

Do you have all the currennt PDF documentation for your version of LifeScope? If not, you really should get that and take some time to read it carefully.

For mapping, the maximum number of jobs is set as a parameter in your *.ini file. So for fragment mapping, you can add a line with "fragmap.max.number.of.jobs=xxxx" where xxxx is a number between 24 and 1000 (the default is 100).

Note though that setting also depends on the machine and resources you are running the mapping on. Another configuration setting is "mapping.memory" which I think defaults to 15Gb, but if you have more you should change that as with 15Gb most (well, mammalian anyway) reference genomes will have to be split up, thereby increasing even further the number of mapping jobs that must be run (and you risk getting poor mapping results anyway by using a split reference genome).

I run LifeScope 2.5.1 on a 4-compute node Penguin cluster with 24Gb of RAM per node. I set "mapping.memory=22" (note that on a cluster this is set up globally, along with other resource settings, in your install.conf file), but I have never had to increase the maximum number of jobs even with runs using 96 barcodes and many samples, so I suspect your problem may be memory limitations and LifeScope needing to split the reference genome?

Just what kind of machine are you doing this on, and how much RAM does it have? I have no experience running LifeScope on anything but Linux and a cluster configuration, so if you are running it on a windows workstation, I may be of no or little further help, sorry.
__________________
Michael Black, Ph.D.
ScitoVation LLC. RTP, N.C.
mbblack is offline   Reply With Quote
Reply

Thread Tools

Posting Rules
You may not post new threads
You may not post replies
You may not post attachments
You may not edit your posts

BB code is On
Smilies are On
[IMG] code is On
HTML code is Off




All times are GMT -8. The time now is 09:22 PM.


Powered by vBulletin® Version 3.8.9
Copyright ©2000 - 2020, vBulletin Solutions, Inc.
Single Sign On provided by vBSSO