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milaboratory / mixcr

MiXCR is an ultimate software platform for analysis of Next-Generation Sequencing (NGS) data for immune profiling.
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Merged runs- different number of clones #248

Closed innagsc closed 6 years ago

innagsc commented 7 years ago

I have a library that has been sequenced on a HiSeq rapid mode (2 lanes/runs). When I ran it through the MiXCR analysis for each run individually, I got the same number of clones for each sample. However, when I merged the Fastq files and ran it through the MiXCR analysis, there were some samples where I got more or fewer clones than for the individual runs.

I will give an example: Run1- sample4 -1854 clones Run2- sample4 - 1854 clones Merged run (concatenating the fastq files for each sample) - sample4 - 1851 clones

Any ideas?

Thank you in advance!

dbolotin commented 6 years ago

Sorry for the extremely delayed response. Such behaviour may be observed due to the error-correction algorithms applied on the assemble step. E.g. having the information combined from two samples, MiXCR manages to eliminate more artificial diversity.