indrop_v1_2.xml

<config>
    <!-- droptag -->
    <TagsSearch>
        <protocol>indrop</protocol>
        <SpacerSearch>
            <spacer>GAGTGATTGCTTGTGACGCCTT</spacer>
            <max_spacer_edit_distance>3</max_spacer_edit_distance>
            <spacer_search_length>4</spacer_search_length>

            <barcode1_min_length>8</barcode1_min_length>
            <barcode1_max_length>11</barcode1_max_length>
            <barcode2_length>8</barcode2_length>
            <umi_length>8</umi_length>
            <r1_rc_length>8</r1_rc_length>
        </SpacerSearch>

        <Processing>
            <min_align_length>10</min_align_length>
            <reads_per_out_file>100000000</reads_per_out_file>
            <poly_a_tail>AAAAAAAA</poly_a_tail>
        </Processing>
    </TagsSearch>

    <!-- dropest -->
    <Estimation>
        <Merge>
            <barcodes_file>indrop_v1_2_barcodes.txt</barcodes_file>
            <barcodes_type>indrop</barcodes_type>
            <min_merge_fraction>0.2</min_merge_fraction>
            <max_cb_merge_edit_distance>2</max_cb_merge_edit_distance>
            <max_umi_merge_edit_distance>1</max_umi_merge_edit_distance>
            <min_genes_after_merge>100</min_genes_after_merge>
            <min_genes_before_merge>20</min_genes_before_merge>
        </Merge>

        <PreciseMerge>
            <max_merge_prob>1e-5</max_merge_prob>
            <max_real_merge_prob>1e-7</max_real_merge_prob>
        </PreciseMerge>
    </Estimation>
</config>