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?
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?
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