de novo contigs don't match mapped reads

[bdorsey]

Hi all,

I'm confused about the results I get when I map the reads back to the contigs from Abyss. There are a number of contigs where the majority of reads have a different base than the contig at a given position. I don't understand how the assembler would assign a base to a position if it is not supported by the reads.

Thanks for any explanations.

Cheers,
BD

[SylvainL]

Hi,

maybe you have more reads supporting the base at this position than reads which don't support it? Different possibilities to check this: the fastest (if you already have a pipeline for) would be to do a fast SNP calling using your contigs as reference...

s.