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Old 09-26-2012, 06:19 PM   #1
oliviaxinw
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Default Too little reads mapped back to contigs using Bowtie

Hi,

I assembled Illumina 100bp reads with Velvet after quality trimming (so all the reads are pretty high quality). I used bowtie to map the reads back to the contigs using paired-end option with a maximum mismatch of 3.

Only 35% of the reads mapped to contigs no matter how large a insert size limit I set.
I tried mapping the reads as single reads rather than paired-end and 50% reads mapped. This is still lower than the percentage of reads used to make the contigs.

What could be the problem with this mapping?

Last edited by oliviaxinw; 09-27-2012 at 05:40 PM.
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Old 09-27-2012, 06:53 AM   #2
westerman
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Will I be better off mapping the reads not as read-pairs but as individual reads?
Yes. At least then you should be able to tell if all of your reads do map.
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Old 09-27-2012, 04:24 PM   #3
oliviaxinw
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I mapped read 1 as non-paired end reads and 50% read mapped to contigs. This is still less than the amount of reads that are used to make the contigs.
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Old 09-27-2012, 09:54 PM   #4
upendra_35
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Quote:
Originally Posted by oliviaxinw View Post
I mapped read 1 as non-paired end reads and 50% read mapped to contigs. This is still less than the amount of reads that are used to make the contigs.
My gut feeling is that the k-mer size you chose to build your assembly is not efficient enough. Perhaps you should optimize your k-mer size to efficiently use most of your reads. Hope this helps....
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Old 09-28-2012, 05:18 AM   #5
arolfe
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Do you know how big the target genome was? What's the total size of your contigs? Maybe your assembly didn't cover the whole genome. Or it's possible that you sequenced a lot of reads from some kind of contaminant or artifact that won't map properly.

Have bowtie give you a file of reads that didn't map, then try two things:
1) is there a lot of duplication in that file? eg, maybe most of the unmapped 50% is some artifact like adapter-dimers
2) use blast on a subset of the unmapped reads to figure out whether this is a Bowtie problem (eg, indel in read prevents mapping) or whether the reads really have no overlap with your assembly.

Alex
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