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  • SHRiMP doubts

    Hi
    I have started using SHRiMP mapping tool. And following are few doubts.

    1. Do I have convert solexa reads into fasta format and then run command as below:
    ../SHRiMP_1_2_0/bin/rmapper-ls -s 111111011111 -n 3 -w 35 -o 20 -r 32 -d -1 -h 2675 test1.txt /../hg18/*.fa > ../results/test1.out


    If I don't convert solexa sequence into fasta format (i.e appending '>' in the beginning of the sequence) then
    Code:
    python ../SHRiMP_1_2_0/utils/splitreads.py 1000 read1.fasta
    does throw some error and I convert the reads into fasta format, then I am able to split the sequence file insto 1000 sequences per file.

    But I get an error when I try to run rmapper-ls as below
    ../SHRiMP_1_2_0/bin/rmapper-ls -s 111111011111 -n 3 -w 35 -o 20 -r 32 -d -1 -h 2675 test1.txt /../hg18/*.fa > ../results/res.0_to_999.out

    Loading reads...error: read [NATGATGCAGGAACATAAAGGACTGGTCATCTTGG] had no sequence!

    Hence I changed the read format as below:
    ATGCATGCGCATCGATCGATCGT
    ATCGTACGATCGTACGTACGTAG
    ..

    and run rmapper but the results are as below:

    General:
    Reads Matched: 0 (0.0000%)
    Total Matches: 0
    Avg Hits/Matched Read: 0.00
    Duplicate Hits Pruned: 0
    Please let me know the input query sequence format? Thanks.
    Last edited by seq_GA; 06-11-2009, 11:53 PM.

  • #2
    Originally posted by seq_GA View Post
    Hi
    I have started using SHRiMP mapping tool. And following are few doubts.
    1. Do I have convert solexa reads into fasta format and then run command as below:
    ../SHRiMP_1_2_0/bin/rmapper-ls -s 111111011111 -n 3 -w 35 -o 20 -r 32 -d -1 -h 2675 test1.txt /../hg18/*.fa > ../results/test1.out
    Please let me know the input query sequence format? Thanks.
    The USAGE section of the Shrimp manual says:

    'rmapper' performs Smith-Waterman alignments of multiple reads
    within one fasta file against one or more reftigs in other fasta files.


    So the reads must be in a SINGLE FASTA file and the reference sequences can be in MULTIPLE FASTA files. FASTQ is not supported. FASTA looks like this:

    >read00001
    AGAGAGGTATATATTTCTCATAGC
    >read00002
    AGGAAGAGAGGTATATATTTCTCA


    Also, your parameter " /../hg18/*.fa " looks wrong.

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