No Bowtie Alignments

Question

[hollynns]

A former lab member assembled a number of contigs from Illumina reads using SPAdes. I have been trying to assess the depth of coverage using Bowtie2 when I noticed something interesting. I find that there are no Bowtie alignments (concordant or discordant) for the largest contig. Can anyone explain this?

Answer 1

[gyulap]

By default in SPAdes there is an error correction step before the assembly. If you have used the original reads, it is possible that they were not mapped because of the mismatches. Use the corrected reads for mapping with Bowtie.

[hollynns]

I'll try that. Thanks!