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10XGenomics / cellranger

10x Genomics Single Cell Analysis
https://www.10xgenomics.com/support/software/cell-ranger
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Low alignment rate when using fastq generated from bamtofastq #235

Closed malonzm1 closed 7 months ago

malonzm1 commented 7 months ago

Hi,

I had to use cellranger's bamtofastq function for some bam files. Then I used the resulting fastq files for clonotype detection (https://github.com/milaboratory/mixcr). I noticed that the alignment rate was very low (from less than 1% to around 3%). Any thoughts?

Thanks and good day.

elehnert10x commented 7 months ago

Thank you for your interest in Cell Ranger. GitHub Issues are not monitored by our support team. Please e-mail support@10xgenomics.com for support with Cell Ranger or visit our documentation site at https://www.10xgenomics.com/support/software/cell-ranger.