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  • MiRNA collapse

    Hello guys, I work with microRNA illumina data, and I am having problems to collapse those reads.
    I am working with reads from 17 to 25nt.
    I tried to use fastx_collapser for collapse my reads before run Miranda and Pita. But there is some huge number of isomirs, so the collapser output too many reads realated to the same microRNA - redundant data.
    I tried also to use SEED software, that collapses reads accepting some size variation, but it only accepts reads more than 21nt.

    Does any one there knows another way to collapse mirna data?

    I am trying to use bowtie for doing this by creating a reference index for each read, aligning the data on these references and then using samtools for extracting the number of alignments for each reference, but it will take a long time.
    Did anybody run into this problem?

    Thank you

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