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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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Need help with converting old codes to newer version #1505

Closed wwang86 closed 10 months ago

wwang86 commented 10 months ago

Hi, I am really new to MiXCR and have no experience with bio-informatic analysis. I have a code from our previous lab member which was used for ver 3.0.13. I want to see if anyone can help me update the code to be used on ver 4.6.0.

mixcr analyze amplicon -s mmu --starting-material rna --5-end v-primers --3-end j-primers --adapters adapters-present --assemble "-OassemblingFeatures=[VDJRegion]" --export "-p fullImputed" Input_R1.fastq.gz Input_R2.fastq.gz output

mizraelson commented 10 months ago

Hi, So the updated code will look like this:

mixcr analyze generic-amplicon \
    --species mmu \
    --rna \
    --floating-left-alignment-boundary \
    --floating-right-alignment-boundary J \
    --assemble-clonotypes-by "VDJRegion" \
    --impute-germline-on-export \
      input_R1.fastq.gz \
      input_R2.fastq.gz \
      result