Question: No Bowtie Alignments
0
gravatar for hollynns
6.5 years ago by
hollynns0
United States
hollynns0 wrote:

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 • 1.5k views
ADD COMMENTlink modified 6.5 years ago by gyulap20 • written 6.5 years ago by hollynns0
2
gravatar for gyulap
6.5 years ago by
gyulap20
Hungary/Gödöllő/NARIC
gyulap20 wrote:

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.

ADD COMMENTlink written 6.5 years ago by gyulap20

I'll try that.  Thanks!

ADD REPLYlink written 6.5 years ago by hollynns0
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