The 454ContigGraph.txt file output by the GS assembler is exactly the kind of information I am looking for. However, I could not tell from the Roche manual how to visualize the results. Any suggestions?
-
-
There is detailed introduction in the Version2.3's manual:
Genome Sequencer FLX System Software Manual Part C: GS De Novo Assembler – GS Reference Mapper – SFF Tools
1.15.1.12 454ContigGraph.txt
After you run a cDNA aseembly project, look at the actual file and read the manual. It is clear and easy to understand. -
You are referring to this manual file, right?
There is a decription of the "first section" of 454ContigGraph.txt containing the average depth of the alignment per contig. But for the "second section" containing connections between contigs they only describe the lines starting with "C" not the ones starting with "I" or with "F". Does anyone know where I can find a description for these parts of the "second section"?
And does anyone know a way to visualize (parts of) this graph structure?
ThanksComment
-
Yes. It is that manual.
In my file, there are "S" and "I" starting instead of "F" and "I".
Here is an example:
S 1 3694 618:+;561:-;560:+;82:-;711:-;500:+
I 164 AGAGGCTTAgggtttttCATCCAATCaaacAGTGCCAGACCACGGTTACACAACAGAACCGATGGCCTCAGCCGGTAACAGGATGGATACCAacagggtgg
I 502 GC 301:875-3'..855-3';6:970-5'..855-3';2867:971-5'..855-3';5:972-5'..855-3'
Couldn't find the explantation from the manual. I think programmer from 454 can explain this.Comment
-
You may develop a program to visualize this.Originally posted by seqseq View Post
I am thinking of doing this... who else is interested?Comment
-
I don't know if it is correct but what i suppose looking at my 454ContigGraph-file:
S isotig-id isotig-length contigs_in_isotig(with direction +/-)
I contig_id consenus_sequence coverage-depth:contigs_surrounding_the contig (???) (leading zeros in the contig_id are discarded: 1 = contig00001)
As I'm very unsure about the last entry in the "I-rows" I still don't have a clue why this entry is missing sometimes...Last edited by dschika; 03-29-2010, 07:13 AM.Comment
-
I got the following explanation:
I: reads 'flowing through' the contig, i.e. reads that start in a neighboring contig, flow through the contig, and end in another neighbor again. In the example:
I 502 GC 301:875-3'..855-3';6:970-5'..855-3';2867:971-5'..855-3';5:972-5'..855-3'
310 reads start in contig 875, flow out it's 3' end, into the 5' of the contig you are looking at (502), out of it again at the 3', and into the 3' of contig 855. The '..' kind of represents the contig in question from 5' to 3'.
In this case, the large number of reads flowing through (301, 6, 2867 and 5, respectively) and the short sequence ('GC') point to a tandem repeat/microsat. All reads go into contig 855, which perhaps is high depth and short also?Comment
-
I just posted an entry on the 454ContigGraph.txt file on my blog about newbler:
Cheers,
flxlexComment
-
Hi, that's a good one. Thank you!Originally posted by flxlex View PostI just posted an entry on the 454ContigGraph.txt file on my blog about newbler:
Cheers,
flxlexComment
-
Thanks. Quite a nice blog on technical details.Comment
-
Visualizing 454contiggraph.txt files
I would be very interested in this. You see displays of this at AGBT/other meetings but I have not seen any tools to display this very useful information. I'm not a programmer, so this would be someone else's bag but would love the tool!Originally posted by linikujp View PostComment
-
For anyone finding this old thread, I wrote a program to do just this.Originally posted by henry.gibbons View Post
I posted it at this address:
Comment
-
Researchers using sequencing and genomics tools often have to make trade-offs. They can choose between speed or scale, short reads or long-range information, or targeted panels or a view of the whole transcriptome. New technologies that have been released this year are built to address those tough choices.
We asked six companies the same four questions to learn about their latest products. The new technologies bring a lot to the table, including rethinking sequencing...
Comment