Few contigs map to reads

[a532942]

Hi!
I am trying to obtain the depth coverage of my contigs. They come from the assembly of paired-end Illumina reads, and the assembler used was CLC. The thing is, using bwa, only a third of the contigs mapped to the reads, although they come from the reads!
Why could these be? Is the edit distance too small? How big should it be?

Thanks in advance!


Sorry, I mapped the contigs to the reads. But still, only a third of the contigs were mapped at all, and they were assembled form those reads. is the assembly bad quality?

[Brian Bushnell]

You should be mapping the reads to the contigs, not the contigs to the reads. Mappers are designed for mapping shorter sequences to longer sequences. Also, you can't calculate coverage mapping contigs to reads.