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jts / sga

de novo sequence assembler using string graphs
http://genome.cshlp.org/content/22/3/549
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Q about "default-variants.fa" #85

Closed WeijianYe closed 9 years ago

WeijianYe commented 9 years ago

HI After the step of "SGA assemble", it will generate a fa file named "default-variants.fa" by default. I think it contains some variants described by the structure of the graph. However, I don't know the meaning of the header in this fa file. Could you help me?

header like:

variant-1/1 IGD:0 ITD:0.00321543 MID: 0 InternalCigar:311M 1375 variant-2/1 IGD:0 ITD:0.00348432 MID: 0 InternalCigar:287M 1121 variant-4/1 IGD:0 ITD:0.00369004 MID: 0 InternalCigar:271M 2187

jts commented 9 years ago

Hi Weijan,

A description of these fields can be found here:

https://groups.google.com/d/msg/sga-users/wgjgqccaJSg/yp91O4g8SkYJ

Cheers, Jared

On Tue, Nov 4, 2014 at 4:36 AM, Weijian notifications@github.com wrote:

HI After the step of "SGA assemble", it will generate a fa file named "default-variants.fa" by default. I think it contains some variants described by the structure of the graph. However, I don't know the meaning of the header in this fa file. Could you help me?

header like:

variant-1/1 IGD:0 ITD:0.00321543 MID: 0 InternalCigar:311M 1375 variant-2/1 IGD:0 ITD:0.00348432 MID: 0 InternalCigar:287M 1121 variant-4/1 IGD:0 ITD:0.00369004 MID: 0 InternalCigar:271M 2187

— Reply to this email directly or view it on GitHub https://github.com/jts/sga/issues/85.

jts commented 9 years ago

I'm going to close this, please re-open if you have more questions.

Jared