GS reference Mapper's file

[nicedad]

Hi everyone,
As per gsMapper manual, gs reference mapper reads only SFF files.
my question is how could that happen while we need to map a result of an assembler to a reference. In other words, if I'm not mistaking, we have got first clean, trim, and then assemple reads. then result of all of this will be alignment to a reference. am I right?

This means, we cannot use any of files that result of gs assembler into gs mapper.

Thanks in advance,

[flxlex]

GsMapper actually maps the reads to the reference, building contigs after the mapping. Does that help?

[nicedad]

ic..!. i thought it's vice versa!!!

[nicedad]

I forgot to thank you flxlex for the replay and for you great blog also.