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milaboratory / mixcr

MiXCR is an ultimate software platform for analysis of Next-Generation Sequencing (NGS) data for immune profiling.
https://mixcr.com
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Low alignment rate when using fastq generated from bamtofastq #1427

Closed malonzm1 closed 1 year ago

malonzm1 commented 1 year ago

Hi,

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

Thanks and good day.

mizraelson commented 1 year ago

Its hard to say without knowing the wet-lab details. What cells were used for the sample preparation ? If it is a 10x data - what kit was used? 5' 10x VDJ end? What command did you use for MiXCR analysis? Can you share the report files generated by MiXCR?