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Old 07-29-2011, 09:48 AM   #1
kespen
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Location: USA

Join Date: Jul 2011
Posts: 1
Default amos file format

Hey all,

To preface, for the project I'm involved with I need to extract paired end info from an assembly - that is, for each paired end read: which contigs it connects, and the orientation and distance it suggests.

To this end, I've assembled on Velvet, created an AMOS file, and then created files for each individual contig from this (using the asmbly_splitter script). However, I'm having trouble interpreting the format of the file, and I've found very little documentation.

For example, the file output looks like:
{TLE
src:5769434
off:327
clr:0,94
}

Can anyone help me understand what these results represent? And how to extract the information I need from this?

Thanks
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Old 08-12-2011, 08:18 AM   #2
mtor.signaling
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Default

Hi kespen,
The TLE field pertains to the mapping of the read (in your case, read # 5769434), to the consensus sequence.
Hopefully this link shall help: http://www.cbcb.umd.edu/research/con...entation.shtml
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