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