Any Substitution For Genemapper?

Question

[wjidea]

Hi friends,

I am working on a population genetic project using microsatellite markers. Due to the large sample size and 12 microsatellite loci, I will need to use an efficient and solid method/tool to score the fragment analysis data (.fsa file type) from genetic analyzer 3130. In total, I will have nearly 5000 files to be scored. I have done part of my pilot fragment analysis results with a free version software, PeakScanner 1.0 (ABI); however, this software doesn't come with automatic features, and thus I have to score the data manually, which is very time consuming and inconvenient. In addition, we don't have the budget to purchase some commercial softwares (such as, Gene Mapper ) to do this. I am wondering if you guys can give me some suggestions to handle this situation.

OR

I can keep the question short, any substitution software package for ABI GeneMapper to score multiplex fragment analysis data (*.fsa)?

Thank you very much.

[ruru]

hi. do u have bioinformatician in your lab? probably u can get them by writing a script to help you analyze the large data size. Or, you try to find any service provider that offer SSR data analysis service using Gene Mapper.

[wjidea]

Thanks, actually I wanted to know the software package to automatically score my Fragment analysis data set.

[wjidea]

OK, a follow-up to my own question. Eventually, I decided to use the PeakScanner V2.0 (which is similar to V1.0) for calling allele sizes for ABI sequencer raw data set. The multiple copies and multiple pastes tool seems to be very efficient for recording allele sizes in the Peakscanner software. Once you have all the raw allele sizes, you will need to run an allele-binning (I was using Tandem) process, which will help you reduce the noise of allele size calling.

Anyway, this could be my last time to work with microsatellite data set. Genome-wide variants should be the future for genotyping techniques.

Good luck!

-J

Answer 1

[cova_ruber]

Update for this question:

There's a package called Fragman in R just released in 2015, performs fragment analysis using FSA files: https://cran.r-project.org/web/packages/Fragman/

Answer 2

[etienneloire]

Hi, I would be interested too. Only proprietary software seems to handle *.fsa files? That's an outrage !

So just in case, any luck since asking the question ?

Cheers

Answer 3

[griley5000]

NCBI has an STR analysis tool that will do fragment analysis, OSIRIS. Analysis of large data sets in .fsa or .hid format is fast and export of allele sizes is straightforward and flexible. OSIRIS is free and open source download available for both Macintosh and Windows. https://www.ncbi.nlm.nih.gov/osiris/
https://www.ncbi.nlm.nih.gov/osiris/download/