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Old 06-10-2009, 01:07 PM   #1
tshea
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Location: cambridge, ma

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Default euler-sr scaffolding

I see that mateTransformGraph has a -scaffold option:

[-scaffold] Use mate-pairs to scaffold disconnected contigs.

Is there a way to obtain fasta sequence of the resulting scaffolds? Or is there documentation to explain how one might parse any of the .graph or .edge or .path files with the goal of constructing a scaffolds fasta file?

Thanks much.
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Old 06-10-2009, 02:38 PM   #2
mchaisso
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Quote:
Originally Posted by tshea View Post
I see that mateTransformGraph has a -scaffold option:

[-scaffold] Use mate-pairs to scaffold disconnected contigs.

Is there a way to obtain fasta sequence of the resulting scaffolds? Or is there documentation to explain how one might parse any of the .graph or .edge or .path files with the goal of constructing a scaffolds fasta file?

Thanks much.
The contigs from the scaffold should be in the "reads.fasta.contig" file that is output at the end of assembly, where "reads.fasta" is the input file. If there is no reads.fasta.contig, the assembly crashed (somebody may be posting an updated scaffolder soon).
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Old 06-11-2009, 11:27 AM   #3
tshea
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Quote:
Originally Posted by mchaisso View Post
The contigs from the scaffold should be in the "reads.fasta.contig" file that is output at the end of assembly, where "reads.fasta" is the input file. If there is no reads.fasta.contig, the assembly crashed (somebody may be posting an updated scaffolder soon).
Thanks Mark.

The assembly did finish and there is a reads.fasta.contig file.

To clarify, is there a way to obtain a fasta file of the scaffolds themselves (linked contigs separated by the estimated number of N's in the gap). I assume that even after the mateTransformGraph stage there are still contigs which, while not overlapping, are at least linked by multiple paired reads (in my case we have 4kb pairs).

You mentioned there may be an updated scaffolder soon - is there something at present that determines and prints out scaffold fasta sequence?

Thanks again.
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