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Extremely high rate of incorrect barcodes observed (99.81 %).

Posted By: dridk, on Mar 4, 2019 at 9:51 AM

Hi,

 

I tried to run longranger targeted on demultiplexed data from MiSeq Illumina.

I m using Illumina index for demultiplexing, not 10x genomics index.

I launch the following command :

 

 

longranger targeted --id=runtest \
                 --reference=refdata-b37-2.1.0 \
                 --fastqs=10x/sacha/outs/fastq_path \
                 --targets=gene.bed \
                 --vcmode=freebayes \
                 --sample=SAMPLE14168

 

 

After a small time, I get the following error :

 

[error] Extremely high rate of incorrect barcodes observed (99.81 %). Check that input is 10x Chromium data, and that there are no missing cycles in the first 16bp of Read 1. Please note Long Ranger 2.0 and above do not support GemCode data.

 

It seems it comes from trimming :

 

2019-03-04 18:21:38 [runtime] (failed)          ID.test2.BASIC_CS.BASIC.TRIM_READS

Any idea where does it come from ? What can I check to find the origin of problem ?

 

 

1 Reply

Re: Extremely high rate of incorrect barcodes observed (99.81 %).

Posted By: shauna-10x, on Mar 5, 2019 at 8:54 AM

Hi,

 

I've contacted our support team and since this issue may require additional investigation, I have opened a support ticket on your behalf using the email associated with your community account. 

 

Best,

Shauna