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Old 10-19-2012, 09:46 AM   #1
themerlin
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Default Opgen MapSolver output to fasta scaffold?

Greetings,

I'm trying to close a genome using optimal maps and sequence data. I have mapped my contigs to the Whole Genome Map and was hoping to try and close gaps in the scaffold. I know that MapSolver currently doesn't have the functionality to export a scaffold based on the map, but was wondering if anyone has figured out a way to create a fasta scaffold based on information in the Placement Report.

thank you,

Jason
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Old 10-20-2012, 08:24 PM   #2
krobison
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It is pretty remarkable that OpGen doesn't provide this, especially when a workable one can be written in a page of Perl or Python. I'm a bit too tired to do so tonight, but here is an outline (maybe next week I'll actually throw this together & post it)

1) Read the MapSolver placement report file -- there is a one line header and then tab-delimited lines with the information of interest; stop scanning when you hit a blank line (there are later pieces with other information).
2) Parse the lines just read. Optical map id is column 0, start and end on map are columns 1 & 2, contig id in column 3 (plus mapping method; need to strip this out by removing 1st space and everything afterwards), start & end positions of contig are columns 4 & 5 and the orientation in column 6. If placement did not include entire contig, need to decide whether to truncate contig to what MapSolver liked OR cram entire piece in
4) Generate list of contigs plus the intervening gaps. If MapSolver thinks they overlapped, need to decide whether to still pad with a gap or not
5) Read in FASTA file with contigs, saving those that are needed; trim & reverse complement as needed
6) Build scaffold(s)
7) Write scaffold(s)

SIMPLE! :-)

Bio::SeqIO & Bio::Seq will be essential for doing this in Perl
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Old 10-21-2012, 07:49 AM   #3
themerlin
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Thanks for your reply. I figured that there was a solution, but I didn't want to re-invent the wheel if someone had already written something that works. I will start writing a script following your work flow. Thank you.

Jason
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Old 09-11-2014, 11:27 AM   #4
yuchengzhang86
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Quote:
Originally Posted by themerlin View Post
Thanks for your reply. I figured that there was a solution, but I didn't want to re-invent the wheel if someone had already written something that works. I will start writing a script following your work flow. Thank you.

Jason
Hi Jason, have you found the solution to use mapsolver map to produce the scaffold? Would you mind sharing it with me? Thanks
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Old 09-11-2014, 11:29 AM   #5
yuchengzhang86
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Quote:
Originally Posted by krobison View Post
It is pretty remarkable that OpGen doesn't provide this, especially when a workable one can be written in a page of Perl or Python. I'm a bit too tired to do so tonight, but here is an outline (maybe next week I'll actually throw this together & post it)

1) Read the MapSolver placement report file -- there is a one line header and then tab-delimited lines with the information of interest; stop scanning when you hit a blank line (there are later pieces with other information).
2) Parse the lines just read. Optical map id is column 0, start and end on map are columns 1 & 2, contig id in column 3 (plus mapping method; need to strip this out by removing 1st space and everything afterwards), start & end positions of contig are columns 4 & 5 and the orientation in column 6. If placement did not include entire contig, need to decide whether to truncate contig to what MapSolver liked OR cram entire piece in
4) Generate list of contigs plus the intervening gaps. If MapSolver thinks they overlapped, need to decide whether to still pad with a gap or not
5) Read in FASTA file with contigs, saving those that are needed; trim & reverse complement as needed
6) Build scaffold(s)
7) Write scaffold(s)

SIMPLE! :-)

Bio::SeqIO & Bio::Seq will be essential for doing this in Perl
Hi Krobison, I'm not good at programming. Do you have any script to produce scaffold fasta file using mapsolver's output? Thanks a lot.
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