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  • BWA and Velvet : Anamolies in contigs and read mapping to reference

    Hi All

    I believe I have an interesting problem to look at or may be its just me who is experiencing this for the first time.

    I have reads from GA for a bacterial genome. I used BWA to map them to known reference. Only 4% reads map back. Seeing the low % I decided to de novo assemble the reads using Velvet .


    1. Total of 2150 contigs
    2. 601 align to reference using 52 % reads from the original set.
    3. k-mer size I used was 29. (read length : 50 bp PE)

    I am not sure what to infer from these very contrasting numbers according to me. With Velvet contigs I am able to use 52% of the reads that aligns well to reference whereas with BWA only 4% reads align.

    Looking forward for your thoughts.

    Thanks!
    -Abhi
    Last edited by apratap; 01-19-2010, 09:35 AM. Reason: typo in subject line

  • #2
    What is the percent identity between the contig and the known reference?

    Comment

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