Update quickstart.rst

milaboratory · Feb 14, 2018 · e547bbe · e547bbe
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commit e547bbe
Showing 1 changed file with 1 addition and 1 deletion.
diff --git a/doc/quickstart.rst b/doc/quickstart.rst
@@ -177,7 +177,7 @@ For the full length cDNA-based immunoglobulin repertoire analysis we generally r
   ::
   
     > mixcr align -p kaligner2 -s hsa -r alignmentReport.txt -OreadsLayout=Collinear \
-      -OvParameters.geneFeatureToAlign=VTranscript read_R1.fastq.gz read_R2.fastq.gz \
+      -OvParameters.geneFeatureToAlign=VTranscriptWithP read_R1.fastq.gz read_R2.fastq.gz \
       alignments.vdjca
      
   Option ``-s`` allows to specify species (e.g. homo sapiens - ``hsa``, mus musculus - ``mmu``). Parameter ``-OreadsLayout`` allow us to set paired-end reads orientation (``Collinear``, ``Opposite``, ``Unknown``). Note, that after MiGEC analysis paired-end read pairs are in ``Collinear`` orientation.