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?
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Originally posted by sewellh View PostI am mapping the reads used to make the contigs back on to the contigs. I get alignments for all contigs except for the largest one. I have BLASTED the contig and it is what I expect.
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1) Have you verified that all of the contigs have unique, correctly-formatted names?
2) Does the contig look normal to you - high complexity, mainly defined bases, rather than e.g. a homopolymer or mostly-N sequence?
3) Is it possible that this contig is a replicate of other contigs? Even though it's bigger, it could be fully covered by other contigs. So, do any other contigs map to it?
4) Is it highly repetitive such that reads aligning to it might exceed the maximum number of allowed alignments?
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Yes, the contigs have uniqe and correctly formatted names. But even when I try to just map the reads to the single large contig, I get no matches.
It doesn't look like this contig is a replicate of others but it does have a 3-4 copies of a ~500 nt fragment within itself. Does that mean that this contig was made incorrectly or that there is something else I should do? I would would expect that if I tried to align the raw reads just to single contig that I would get some alignments.
Update: Using the resulting fastq files from the Hammer error correcting, I still get no Bowtie alignments to that contig
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Thanks so much for your help. I'll try out BBMap. If you are curious at all to look at the contigs, they're on JGI. The largest is:
>gi|589096183|gb|JARN01000011.1| Dehalococcoidia bacterium DscP2 WGS:JARN01:comHGAPfinal_Contig11_1.11, whole genome shotgun sequence
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