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No Bowtie Alignments

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?

alignment next-gen assembly
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updated by Ram Ram • written by hollynns • hollynns

1 answer

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.

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written by gyulap • gyulap

I'll try that. Thanks!

• 1 views • link
updated by Ram Ram • written by hollynns • hollynns

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