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  • Kennels
    replied
    Problem solved.

    I was assuming that paired information was deduced and included in the amos .afg file during its generation, but actually the paired information must be explicitly provided in a separate .mates file. Once this was included in the .afg file generation, I could run minimus -> bambus -> hawkeye to view any scaffolds.

    I found a really helpful site which provided a script to parse out the mate pair information from your input .fasta file here http://compbio.korea.ac.kr/wiki/inde...ina_for_bambus which is this:

    Code:
    cat my.fasta |grep ">" |sed s/\>//g |sed 's/\/1*$/./g;s/\/2*$/./g'|awk -F "." '{print $1}' |sort |uniq -c |awk '{if ($1 == 2) print $2"/1\t"$2"/2\tsmall"}' > mates.txt
    One just needs to adjust and add the library name and insert sizes at the top of the generated file.

    Leave a comment:


  • Kennels
    replied
    I have, but still waiting for reply, and hoped to reach a wider audience here.
    Anyone any ideas?

    Leave a comment:


  • suryasaha
    replied
    You might try asking this on AMOS HELP <[email protected]>. You can sign up here.

    -S.

    Leave a comment:


  • AMOS: problem getting hawkeye to view bambus output

    Hi,

    Does anyone have an idea what my problem is? I've just installed and learning to use AMOS.
    I'm using AMOS's minimus to assemble some .fasta reads, make scaffold by Bambus2, and try to visualize in hawkeye.

    My workflow was:
    1. toAmos -s myreads.fa -o myreads.afg
    2. minimus myreads.afg
    3. goBambus2 myreads.bnk/ myScaff

    Everything ran with no problem up to this point. Then,

    4. hawkeye myreads.bnk

    I got the follow error:

    Opening myreads.bnk/... [0.00s]
    Indexing Contigs .......... [0.00s] 712 reads in 15 contigs
    Indexing Scaffolds [0.00s] 0 contigs in 0 scaffolds
    Indexing Libraries .......... [0.00s] 2 libraries
    Indexing Mates .......... [0.00s] 22 mated reads in 772 fragments
    Indexing Reads .......... [0.00s] 714 reads
    Features not available
    Initialize Display .ERROR: WHAT: Cannot stream fetch: beyond end of stream
    LINE: 147
    FILE: BankStream_AMOS.cc

    My fasta sequence reads is just a compilation of reads from various lanes of illumina data. It may not have pair end information for all reads.
    Is my error due to not having paired end information? If so why did Bambus2 run with no errors?

    Thanks

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