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Old 09-24-2015, 01:05 PM   #1
bdorsey
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Location: USA

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Default de novo contigs don't match mapped reads

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
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Old 09-24-2015, 11:39 PM   #2
SylvainL
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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.
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