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  • asifemon
    replied
    [QUOTE=bio-x;6068]

    usage: $0 [options] -l libraryname -s seq.fasta -q qlt.fasta > new.frg

    can someone give me a complete exampe to run this command.

    Leave a comment:


  • sklages
    replied
    Probably,
    Code:
    convert-fasta-to-v2.pl
    taken from resource mentioned above ..

    cheers,
    Sven

    Leave a comment:


  • dan
    replied
    Originally posted by bio-x View Post
    usage: $0 [options] -l libraryname -s seq.fasta -q qlt.fasta > new.frg
    What is $0 ?

    Leave a comment:


  • bio-x
    replied
    hi, you can try the following,

    usage: $0 [options] -l libraryname -s seq.fasta -q qlt.fasta > new.frg
    -v vector-clear-file A file of 'readUID vecBeg vecEnd', one per line, that is the vector clear range.
    -noobt Set the 'doNotOverlapTrim' library feature.
    -454 Set library features appropriate for 454 reads (see also sffToCA).
    -idregex pattern Use this perl regex to extract the read name from the seq defline.
    -l libraryname Name of the library; freeformat text.
    -mean m Insert has mean size of m.
    -stddev s Insert has std dev of s.
    -s seq Fasta file of sequences.
    -q qual Fasta file of quality values.
    -m matepairing A file of pairs of read UIDs for mated reads, one pair per line, whitespace separated

    Leave a comment:


  • dan
    replied
    Cheers Sven,

    That looks like a great resource!


    Dan.

    Leave a comment:


  • sklages
    replied
    @gengen,

    Have a look at Celera Input Formatting

    Sven
    Last edited by sklages; 06-21-2009, 02:13 AM. Reason: multiple issues in one thread

    Leave a comment:


  • novice2
    replied
    To all members

    I have attached a further 2 images showing this effect.
    Attached Files

    Leave a comment:


  • novice2
    replied
    To all members

    Dear All

    My pcr assay has suddenly began producing these curious strutures-- I have attached an image to show this effect. Can anyone explain please what mat be going on and what I can do to get rid of it. Before this the pcr was working fine.
    Attached Files

    Leave a comment:


  • gengen
    replied
    How to create frg file from SRA data ?

    I want to run Celera Assembler usign SRA 454 data, but SRA doesn't provide sff data. They only provide FASTA and FASTQ.
    So, how should I do ? I could do this by coverting FASTQ to FASTA and quality file and then converting them to frg file, but this is so roundabout and also I must write some scripts. Let me know if you have any idea for this issue.

    thanks in advance
    Last edited by gengen; 06-20-2009, 08:24 PM. Reason: mistype

    Leave a comment:


  • dan
    replied
    Originally posted by new300 View Post
    Are you planning to use the Celera assembler with short reads? Because I don't think it would work very well.
    Have a look here,

    Discussion of any scientific study related to high content or next generation genomics. Whole genome association, metagenomics, digital gene expression, etc.

    Leave a comment:


  • sklages
    replied
    Code:
    pair    \W+\.b\.abi    \W+\.g\.abi
    If this is a perl RE "\W+" means, "everything but chars, digits and _"; that is
    probably not what you want.

    Your sample name looks like this: 065I03X00001.b.abi

    better this way (\t as separator):
    Code:
     pair  (.*)\.b\.abi$ (.*)\.g\.abi$
    hth,
    Sven

    Leave a comment:


  • dan
    replied
    I should try before I reply... Setting test.mates to

    Code:
    pair	\.b\.abi	\.g\.abi
    Seems to have had the desired effect!

    Now I just need to rerun the assembly and check in hawkeye.

    Leave a comment:


  • dan
    replied
    Sadly it doesn't seem to be working...

    Code:
    toAmos -s x.fasta -q x.qual  -o a.afg
    Code:
    toAmos -s x.fasta -q x.qual -m test.mates -o b.afg

    Gives:

    Code:
    diff a.afg b.afg
    5c5
    < Thu Dec  4 12:24:40 2008
    ---
    > Thu Dec  4 12:27:07 2008
    Following the info on the link I set test.mates to the following:

    Code:
    pair	\W+\.b\.abi	\W+\.g\.abi
    Their is no error on either command.

    Leave a comment:


  • sklages
    replied
    Yeah, that's what I wanted to send just about now


    Btw,. I meant Bambus *input* not output ...

    cheers,
    Sven

    Leave a comment:


  • dan
    replied
    Seems the Bambus docs will help:

    Leave a comment:

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