unable to parse out UMI
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liuyang218622 commented
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?