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  • alvin
    Junior Member
    • Oct 2010
    • 9
    #1

    Mapping and counting, small RNA seq. GA IIX

    Hi all!
    The size of my sequences are between 17-68 pb and I would like to align them to the genome with bowtie or bwa. Indeed, these sequences are from a Protozoa specie.
    I haven't run these programs before so I don't know what are the best parameters.
    I use to run cross match and I may say that the best parameters for small RNAs were:
    cross_match -masklevel 0 -minmatch 8 -maxmatch 14 -minscore 14 -gap1_only -globality 3 -minmargin -0.5
    but it's hard to find the same parameters in bowtie and bwa.
    I wonder if anyone has experience with bowtie and bwa parameters with small RNA sequences from Illumina.
    In addition, I would like to know if there is some program for counting, I mean I would like to know how many reads match with a gene, etc.
    I would really appreciate your help.
    Thanks in advance.


    alvin
    Tags: illumina, rna, rna-seq, small non coding rna, small rna sequencing
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