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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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Takara Smarter Seq #1791

Closed bshim181 closed 2 months ago

bshim181 commented 2 months ago

Hello,

I have tried running the Takara Smarter Seq through MiXCR's preset and but struggling to get sufficient clone counts due to high proportion of reads getting discarded due to failed mapping in assembly.

Alignment itself is not optimal, but I am seeing approximately 60% of reads aligning.

Screenshot 2024-09-13 at 12 02 03 PM

Reads used in clonotyping are only showing 6% with 40% of the reads dropped due to failed mapping. What might be the cause for this? Is there additional parameters required for the Takara smarter seq preset to process the data correctly?

Screenshot 2024-09-13 at 12 00 48 PM
mizraelson commented 2 months ago

It seems like the sequencing quality is low and that is why MiXCR filters out those reads.