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unable to parse out UMI #134

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liuyang218622 opened this issue Sep 6, 2022 · 0 comments
Open

unable to parse out UMI #134

liuyang218622 opened this issue Sep 6, 2022 · 0 comments

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@liuyang218622
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liuyang218622 commented Sep 6, 2022

my data is 10x v3 data, I change the config file to umi length equal to 12 ,but it also reported that “unable to parse out UMI “,

Below is the command line that I write:
dropest -V -C 6000 -m /home/liuyang/01.example_script/02.cellranger/refdata-gex-GRCh38-2020-A/genes/genes.gtf -c ./dropEst/configs/10x_v3.xml ../01.rawdata/01.bam_file/sample1/sample1.bam
I got the error “unable to parse out UMI;
The 10x_v3.xml is:



10x

<barcode1_length>8</barcode1_length>
<barcode2_length>16</barcode2_length>
<umi_length>12</umi_length>
<r1_rc_length>0</r1_rc_length>

    <Processing>
        <min_align_length>10</min_align_length>
        <reads_per_out_file>10000000</reads_per_out_file>
        <poly_a_tail>AAAAAAAA</poly_a_tail>
    </Processing>
</TagsSearch>

<!-- dropest -->
<Estimation>
    <Merge>
        <barcodes_file>../data/barcodes/10x_aug_2016_split</barcodes_file>
        <barcodes_type>const</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>

can someone can tell me how I can fix the error?

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