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    <h2>miRNA-seq / Convert miRBased BAM file to count table</h2>

    <h3>Description</h3>

    <p>
        This tool takes a BAM file as an input, calculates the number of times each miRNA
        is identified, and removes the ones for which the count is under the user defined threshold.</p>

    <h3>Parameters</h3>

    <ul>
        <li>Count limit (0-1000) [10]</li>
    </ul>

    <h3>Details</h3>

    <p>
        The tool takes as input a BAM file with reads that have been aligned against miRBase and counts
        the number of alignments per miRNA sequence. Only reads with single alignment are included in the
        count.</p>
    <p>
        User can define a threshold value for count number to be included.
    </p>

    </p>
    <p>


        <h3>Output</h3>

        <p>
            <ul>
                <li>miRNA-counts.tsv: A count file suitable for differential expression analysis</li>
            </ul>
        </p>


        <h3>References</h3>

        <p>

</body>
<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
<html lang="en">

<head>
    <title></title>
</head>

<body>

    <h2>miRNA-seq / Convert miRBased BAM file to count table</h2>

    <h3>Description</h3>

    <p>
        This tool takes a BAM file as an input, calculates the number of times each miRNA
        is identified, and removes the ones for which the count is under the user defined threshold.</p>

    <h3>Parameters</h3>

    <ul>
        <li>Count limit (0-1000) [0]</li>
    </ul>

    <h3>Details</h3>

    <p>
        The tool takes as input a BAM file with reads that have been aligned against miRBase and counts
        the number of alignments per miRNA sequence. Only reads with single alignment are included in the
        count.</p>
    <p>
        User can define a threshold value for count number to be included.
    </p>

    </p>
    <p>


        <h3>Output</h3>

        <p>
            <ul>
                <li>miRNA-counts.tsv: A count file suitable for differential expression analysis</li>
            </ul>
        </p>


        <h3>References</h3>

        <p>

</body>

Change default count limit to 0.
Change default count limit to 0.