About documentation of corona_lite

ribomics · 11-05-2008, 12:03 AM

Of the three components of corona_lite(matching,pairing,SNPs), "matching" has detail information of analysis results. However, the rest two have not.
Anyone could say something about the results of pairing and SNPs? any further suggestions for subsequent analysis on corona_lite raw analysis data? Thanks very much.
Luo Yingfeng (BIG China).

westerman · 11-05-2008, 09:54 AM

What type of information do you want?

The SNP calling produces a bunch of files.

The most important one in many is the one that contains the SNPs ("snps.txt").

I also find the file that maps all of the reads onto the reference to be useful ("bp_consensus_confirmed_sequence_with_Ns.fasta") in some applications.

The *.gff files are required if you look at the results within the genome browser.

There are also a bunch of files which I do find very useful at all.

ribomics · 11-08-2008, 08:30 PM

Thank your for answer! Do you have SOLiD documentation about that? We have not got documentations for "pairing" and "SNPs" as that for "mapping".

westerman · 11-10-2008, 10:01 AM

The documentation that came with the SOLiD software -- but unfortunately not with the corona lite software found at solidsoftwaretools.com/gf -- lists the output files. A lot of my knowledge has just come from playing around with the corona lite programs. Also email to soliddev@appliedbiosystems.com will sometimes elicit answers.

ribomics · 11-15-2008, 06:19 AM

Thank your very much！

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11-05-2008, 12:03 AM	#1
ribomics Junior Member Location: China Join Date: Mar 2008 Posts: 3	About documentation of corona_lite Of the three components of corona_lite(matching,pairing,SNPs), "matching" has detail information of analysis results. However, the rest two have not. Anyone could say something about the results of pairing and SNPs? any further suggestions for subsequent analysis on corona_lite raw analysis data? Thanks very much. Luo Yingfeng (BIG China).

11-05-2008, 09:54 AM	#2
westerman Rick Westerman Location: Purdue University, Indiana, USA Join Date: Jun 2008 Posts: 1,104	What type of information do you want? The SNP calling produces a bunch of files. The most important one in many is the one that contains the SNPs ("snps.txt"). I also find the file that maps all of the reads onto the reference to be useful ("bp_consensus_confirmed_sequence_with_Ns.fasta") in some applications. The *.gff files are required if you look at the results within the genome browser. There are also a bunch of files which I do find very useful at all.

11-08-2008, 08:30 PM	#3
ribomics Junior Member Location: China Join Date: Mar 2008 Posts: 3	Thank your for answer! Do you have SOLiD documentation about that? We have not got documentations for "pairing" and "SNPs" as that for "mapping".

11-10-2008, 10:01 AM	#4
westerman Rick Westerman Location: Purdue University, Indiana, USA Join Date: Jun 2008 Posts: 1,104	The documentation that came with the SOLiD software -- but unfortunately not with the corona lite software found at solidsoftwaretools.com/gf -- lists the output files. A lot of my knowledge has just come from playing around with the corona lite programs. Also email to soliddev@appliedbiosystems.com will sometimes elicit answers.

11-15-2008, 06:19 AM	#5
ribomics Junior Member Location: China Join Date: Mar 2008 Posts: 3	Thank your very much！